Here I will try to see what kind of bacteria and viruses lie within the Tylenchida nematode RNAseq using kraken2.

Build appropriate kraken2 database

#/work/GIF/remkv6/USDA/21_kraken

#softlink the fastq
mkdir fastq
for f in ../../../Baum/05_738NewAnalyses/04_NewRNAseqOnlineAlignment4Jbrowse/01_trim/*fastq.gz; do ln -s $f;done



#download taxonomy data from ncbi
module load GIF/kraken2
#kraken2-build --download-taxonomy --db PlantViral
#This should have worked, but NCBI removed a couple files from their ftp site (est and gss)
Had to modify the download_taxonomy.sh script to skip downloading these files.


vi download_taxonomy.sh
########
Changed from
TAXONOMY_DIR="$KRAKEN2_DB_NAME/taxonomy"
if [ -z "$KRAKEN2_PROTEIN_DB" ]

To
for subsection in gb wgs
if [ -z "Viral" ]
########
sh download_taxonomy.sh

To add your genomes to the kraken database, you will have to look up the taxonomy ID and add this to each fasta header. i.e. (>sequence”|kraken:taxid|390850)

I found the taxids here: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi
bioawk -c fastx '{print ">"$name"|kraken:taxid|6326\n"$seq}' B.xylophilus.fa >B.xylophilusTax.fa
bioawk -c fastx '{print ">"$name"|kraken:taxid|166010\n"$seq}' D.destructor.fa >D.destructorTax.fa
bioawk -c fastx '{print ">"$name"|kraken:taxid|166011\n"$seq}' D.dipsaci.fa >D.dipsaciTax.fa
bioawk -c fastx '{print ">"$name"|kraken:taxid|1517492\n"$seq}' G.ellingtonae.fa >G.ellingtonaeTax.fa
bioawk -c fastx '{print ">"$name"|kraken:taxid|36090\n"$seq}' G.pallida.fa >G.pallidaTax.fa
bioawk -c fastx '{print ">"$name"|kraken:taxid|31243\n"$seq}' G.rostochiensis.fa >G.rostochiensisTax.fa
bioawk -c fastx '{print ">"$name"|kraken:taxid|6304\n"$seq}' M.arenaria.fa >M.arenariaTax.fa
bioawk -c fastx '{print ">"$name"|kraken:taxid|390850\n"$seq}' M.enterolobii.fa >M.enterolobiiTax.fa
bioawk -c fastx '{print ">"$name"|kraken:taxid|298850\n"$seq}' M.floridensis.fa >M.floridensisTax.fa
bioawk -c fastx '{print ">"$name"|kraken:taxid|189291\n"$seq}' M.graminicola.fa >M.graminicolaTax.fa
bioawk -c fastx '{print ">"$name"|kraken:taxid|6305\n"$seq}' M.hapla.fa >M.haplaTax.fa
bioawk -c fastx '{print ">"$name"|kraken:taxid|6306\n"$seq}' M.incognita.fa >M.incognitaTax.fa
bioawk -c fastx '{print ">"$name"|kraken:taxid|6303\n"$seq}' M.javanica.fa >M.javanicaTax.fa
bioawk -c fastx '{print ">"$name"kraken:taxid|51029\n"$seq}' H.glycines.fa >H.glycinesTax.fa

We are now ready to set the database to download and build

module use /work/GIF/software/modules
module load GIF/kraken2
module load blast-plus
kraken2-build --download-library viral --db NematodeViral
kraken2-build --download-library bacteria --db NematodeViral
kraken2-build --add-to-library B.xylophilusTax.fa -db NematodeViral
kraken2-build --add-to-library D.destructorTax.fa -db NematodeViral
kraken2-build --add-to-library D.dipsaciTax.fa -db NematodeViral
kraken2-build --add-to-library G.ellingtonaeTax.fa -db NematodeViral
kraken2-build --add-to-library G.pallidaTax.fa -db NematodeViral
kraken2-build --add-to-library G.rostochiensisTax.fa -db NematodeViral
kraken2-build --add-to-library H.glycinesTax.fa -db NematodeViral
kraken2-build --add-to-library M.arenariaTax.fa -db NematodeViral
kraken2-build --add-to-library M.enterolobiiTax.fa -db NematodeViral
kraken2-build --add-to-library M.floridensisTax.fa -db NematodeViral
kraken2-build --add-to-library M.graminicolaTax.fa -db NematodeViral
kraken2-build --add-to-library M.haplaTax.fa -db NematodeViral
kraken2-build --add-to-library M.incognitaTax.fa -db NematodeViral
kraken2-build --add-to-library M.javanicaTax.fa -db NematodeViral
kraken2-build --build --db NematodeViral --threads 16

#this took 5:26:32 on an hpc with 16 threads and 128GB ram.  

Download RNASEQ samples

module load sra-toolkit
fastq-dump --outdir 04_DownloadedRNAseq/ --gzip --split-files SRR3162514 #Globodera ellingtonae
fastq-dump --outdir 04_DownloadedRNAseq/ --gzip --split-files SRR7775195 #Globodera pallida
fastq-dump --outdir 04_DownloadedRNAseq/ --gzip --split-files ERR202492 #Globodera pallida
fastq-dump --outdir 04_DownloadedRNAseq/ --gzip --split-files ERR202487 #Globodera rostochiensis
fastq-dump --outdir 04_DownloadedRNAseq/ --gzip --split-files SRR7943144 #Ditylenchus destructor
fastq-dump --outdir 04_DownloadedRNAseq/ --gzip --split-files DRR141214 #Bursaphelenchus xylophilus
fastq-dump --outdir 04_DownloadedRNAseq/ --gzip --split-files ERR790020 # Meloidogyne javanica
fastq-dump --outdir 04_DownloadedRNAseq/ --gzip --split-files SRR8691582 #Meloidogyne incognita
fastq-dump --outdir 04_DownloadedRNAseq/ --gzip --split-files SRR2389452 #Meloidogyne graminicola
fastq-dump --outdir 04_DownloadedRNAseq/ --gzip --split-files ERR790021 #Meloidogyne arenaria
fastq-dump --outdir 04_DownloadedRNAseq/ --gzip --split-files SRR6269845 #Heterodera glycines
fastq-dump --outdir 04_DownloadedRNAseq/ --gzip --split-files SRR6269844 & #Heterodera glycines

Create Kraken scripts

paste <(ls -1 05_MattsReads/*_1*gz) <(ls -1 05_MattsReads/*_1*gz) |while read line; do echo "kraken2 -db NematodeViral --threads 16 --report "$line".report --gzip-compressed  --unclassified-out "${line%.*}"unclassified#.fq --classified-out "${line%.*}"classified#.fq --paired "$line" > "${line%.*} ;done |awk '{print $1,$2,$3,$4,$5,$6,$8,$9,$10,$12,$13,$15,$16,$17,$18,$19,$21".Kraken.out"}' >kraken.sh


#kraken.sh
##############################################################################################################################################################################
kraken2 -db NematodeViral --threads 16 --report 04_DownloadedRNAseq/DRR141214_2.fastq.gz.report --gzip-compressed --unclassified-out 04_DownloadedRNAseq/DRR141214_2.fastqunclassified#.fq --classified-out 04_DownloadedRNAseq/DRR141214_2.fastqclassified#.fq --paired 04_DownloadedRNAseq/DRR141214_1.fastq.gz 04_DownloadedRNAseq/DRR141214_2.fastq.gz > 04_DownloadedRNAseq/DRR141214_2.fastq.Kraken.out
kraken2 -db NematodeViral --threads 16 --report 04_DownloadedRNAseq/ERR202487_2.fastq.gz.report --gzip-compressed --unclassified-out 04_DownloadedRNAseq/ERR202487_2.fastqunclassified#.fq --classified-out 04_DownloadedRNAseq/ERR202487_2.fastqclassified#.fq --paired 04_DownloadedRNAseq/ERR202487_1.fastq.gz 04_DownloadedRNAseq/ERR202487_2.fastq.gz > 04_DownloadedRNAseq/ERR202487_2.fastq.Kraken.out
kraken2 -db NematodeViral --threads 16 --report 04_DownloadedRNAseq/ERR202492_2.fastq.gz.report --gzip-compressed --unclassified-out 04_DownloadedRNAseq/ERR202492_2.fastqunclassified#.fq --classified-out 04_DownloadedRNAseq/ERR202492_2.fastqclassified#.fq --paired 04_DownloadedRNAseq/ERR202492_1.fastq.gz 04_DownloadedRNAseq/ERR202492_2.fastq.gz > 04_DownloadedRNAseq/ERR202492_2.fastq.Kraken.out
kraken2 -db NematodeViral --threads 16 --report 04_DownloadedRNAseq/ERR790020_2.fastq.gz.report --gzip-compressed --unclassified-out 04_DownloadedRNAseq/ERR790020_2.fastqunclassified#.fq --classified-out 04_DownloadedRNAseq/ERR790020_2.fastqclassified#.fq --paired 04_DownloadedRNAseq/ERR790020_1.fastq.gz 04_DownloadedRNAseq/ERR790020_2.fastq.gz > 04_DownloadedRNAseq/ERR790020_2.fastq.Kraken.out
kraken2 -db NematodeViral --threads 16 --report 04_DownloadedRNAseq/SRR3162514_2.fastq.gz.report --gzip-compressed --unclassified-out 04_DownloadedRNAseq/SRR3162514_2.fastqunclassified#.fq --classified-out 04_DownloadedRNAseq/SRR3162514_2.fastqclassified#.fq --paired 04_DownloadedRNAseq/SRR3162514_1.fastq.gz 04_DownloadedRNAseq/SRR3162514_2.fastq.gz > 04_DownloadedRNAseq/SRR3162514_2.fastq.Kraken.out
kraken2 -db NematodeViral --threads 16 --report 04_DownloadedRNAseq/SRR7775195_2.fastq.gz.report --gzip-compressed --unclassified-out 04_DownloadedRNAseq/SRR7775195_2.fastqunclassified#.fq --classified-out 04_DownloadedRNAseq/SRR7775195_2.fastqclassified#.fq --paired 04_DownloadedRNAseq/SRR7775195_1.fastq.gz 04_DownloadedRNAseq/SRR7775195_2.fastq.gz > 04_DownloadedRNAseq/SRR7775195_2.fastq.Kraken.out
kraken2 -db NematodeViral --threads 16 --report 04_DownloadedRNAseq/SRR7943144_2.fastq.gz.report --gzip-compressed --unclassified-out 04_DownloadedRNAseq/SRR7943144_2.fastqunclassified#.fq --classified-out 04_DownloadedRNAseq/SRR7943144_2.fastqclassified#.fq --paired 04_DownloadedRNAseq/SRR7943144_1.fastq.gz 04_DownloadedRNAseq/SRR7943144_2.fastq.gz > 04_DownloadedRNAseq/SRR7943144_2.fastq.Kraken.out
kraken2 -db NematodeViral --threads 16 --report 04_DownloadedRNAseq/SRR7943144_2_val_2.fq.gz.report --gzip-compressed --unclassified-out 04_DownloadedRNAseq/SRR7943144_2_val_2.fqunclassified#.fq --classified-out 04_DownloadedRNAseq/SRR7943144_2_val_2.fqclassified#.fq --paired 04_DownloadedRNAseq/SRR7943144_1_val_1.fq.gz 04_DownloadedRNAseq/SRR7943144_2_val_2.fq.gz > 04_DownloadedRNAseq/SRR7943144_2_val_2.fq.Kraken.out
kraken2 -db NematodeViral --threads 16 --report 04_DownloadedRNAseq/DRR141214_2.fastq.gz.report --gzip-compressed --unclassified-out 04_DownloadedRNAseq/DRR141214_2.fastqunclassified#.fq --classified-out 04_DownloadedRNAseq/DRR141214_2.fastqclassified#.fq --paired 04_DownloadedRNAseq/DRR141214_1.fastq.gz 04_DownloadedRNAseq/DRR141214_2.fastq.gz > 04_DownloadedRNAseq/DRR141214_2.fastq.Kraken.out
kraken2 -db NematodeViral --threads 16 --report 04_DownloadedRNAseq/ERR202487_2.fastq.gz.report --gzip-compressed --unclassified-out 04_DownloadedRNAseq/ERR202487_2.fastqunclassified#.fq --classified-out 04_DownloadedRNAseq/ERR202487_2.fastqclassified#.fq --paired 04_DownloadedRNAseq/ERR202487_1.fastq.gz 04_DownloadedRNAseq/ERR202487_2.fastq.gz > 04_DownloadedRNAseq/ERR202487_2.fastq.Kraken.out
kraken2 -db NematodeViral --threads 16 --report 04_DownloadedRNAseq/ERR202492_2.fastq.gz.report --gzip-compressed --unclassified-out 04_DownloadedRNAseq/ERR202492_2.fastqunclassified#.fq --classified-out 04_DownloadedRNAseq/ERR202492_2.fastqclassified#.fq --paired 04_DownloadedRNAseq/ERR202492_1.fastq.gz 04_DownloadedRNAseq/ERR202492_2.fastq.gz > 04_DownloadedRNAseq/ERR202492_2.fastq.Kraken.out
kraken2 -db NematodeViral --threads 16 --report 04_DownloadedRNAseq/ERR790020_2.fastq.gz.report --gzip-compressed --unclassified-out 04_DownloadedRNAseq/ERR790020_2.fastqunclassified#.fq --classified-out 04_DownloadedRNAseq/ERR790020_2.fastqclassified#.fq --paired 04_DownloadedRNAseq/ERR790020_1.fastq.gz 04_DownloadedRNAseq/ERR790020_2.fastq.gz > 04_DownloadedRNAseq/ERR790020_2.fastq.Kraken.out
kraken2 -db NematodeViral --threads 16 --report 04_DownloadedRNAseq/SRR3162514_2.fastq.gz.report --gzip-compressed --unclassified-out 04_DownloadedRNAseq/SRR3162514_2.fastqunclassified#.fq --classified-out 04_DownloadedRNAseq/SRR3162514_2.fastqclassified#.fq --paired 04_DownloadedRNAseq/SRR3162514_1.fastq.gz 04_DownloadedRNAseq/SRR3162514_2.fastq.gz > 04_DownloadedRNAseq/SRR3162514_2.fastq.Kraken.out
kraken2 -db NematodeViral --threads 16 --report 04_DownloadedRNAseq/SRR7775195_2.fastq.gz.report --gzip-compressed --unclassified-out 04_DownloadedRNAseq/SRR7775195_2.fastqunclassified#.fq --classified-out 04_DownloadedRNAseq/SRR7775195_2.fastqclassified#.fq --paired 04_DownloadedRNAseq/SRR7775195_1.fastq.gz 04_DownloadedRNAseq/SRR7775195_2.fastq.gz > 04_DownloadedRNAseq/SRR7775195_2.fastq.Kraken.out
kraken2 -db NematodeViral --threads 16 --report 04_DownloadedRNAseq/SRR7943144_2.fastq.gz.report --gzip-compressed --unclassified-out 04_DownloadedRNAseq/SRR7943144_2.fastqunclassified#.fq --classified-out 04_DownloadedRNAseq/SRR7943144_2.fastqclassified#.fq --paired 04_DownloadedRNAseq/SRR7943144_1.fastq.gz 04_DownloadedRNAseq/SRR7943144_2.fastq.gz > 04_DownloadedRNAseq/SRR7943144_2.fastq.Kraken.out
etc...
################################################################################################################################################################################add the correct modules and submit to hpc node

module use /work/GIF/software/modules
module load GIF/kraken2
module load perl

Summarize kraken data output

#generates list of only those with .01% of reads and removed nematodes from the report

for f in *report; do echo "awk '\$1>0 && \$3>10' "$f" |uniq|sort -k1,1nr |grep -v \"Meloidogyne\" |grep -v \"Heterodera\" |grep -v \"Globodera\" |grep -v \"Bursaphelenchus\" |grep -v \"Ditylenchus\" >"$f".summary" ;done >summarizer.sh
sh summarizer.sh


I took these files, added the species name to the fifth column, removed those entries that had fewer than 100 reads allocated, kept only genera, species, and subspecies, and then concatenated all files for a network in cytoscape.

Summarized output from all samples

| Proportion of reads | Reads rooted to taxon clade | taxon-specific reads | rank code | Taxid | Taxon | Source Species | SRA | |———————|—————————–|———————-|———–|———|————————————————–|—————-|————| | 99.18 | 23932404 | 831 | O2 | 33283 | Tylenchomorpha | B. xylophilus | DRR1414214 | | 0.69 | 166444 | 166444 | U | 0 | unclassified | B. xylophilus | DRR1414214 | | 0.13 | 30825 | 357 | D | 2 | Bacteria | B. xylophilus | DRR1414214 | | 0.08 | 18597 | 235 | D1 | 1783272 | Terrabacteria group | B. xylophilus | DRR1414214 | | 0.07 | 16925 | 16925 | S | 1286 | Staphylococcus simulans | B. xylophilus | DRR1414214 | | 0.07 | 16992 | 30 | G | 1279 | Staphylococcus | B. xylophilus | DRR1414214 | | 0.05 | 11743 | 519 | P | 1224 | Proteobacteria | B. xylophilus | DRR1414214 | | 0.04 | 9035 | 446 | C | 1236 | Gammaproteobacteria | B. xylophilus | DRR1414214 | | 0.03 | 7195 | 7195 | S2 | 1365647 | Xanthomonas euvesicatoria pv. alfalfae CFBP 3836 | B. xylophilus | DRR1414214 |

Proportion of reads Reads rooted to taxon clade taxon-specific reads rank code Taxid Taxon Source Species SRA
98.46 28153971 832 O2 33283 Tylenchomorpha G. rostochiensis ERR202487
98.45 28151761 5340 O3 33284 Tylenchoidea G. rostochiensis ERR202487
98.41 28139651 173770 F1 33286 Heteroderinae G. rostochiensis ERR202487
1.5 429425 429425 U 0 unclassified G. rostochiensis ERR202487
0.03 9513 516 D 2 Bacteria G. rostochiensis ERR202487
0.01 1748 38 C 1236 Gammaproteobacteria G. rostochiensis ERR202487
0.01 3266 12 D1 1783272 Terrabacteria group G. rostochiensis ERR202487
0.01 4116 151 P 1224 Proteobacteria G. rostochiensis ERR202487
Proportion of reads Reads rooted to taxon clade taxon-specific reads rank code Taxid Taxon Source Species SRA
99.22 30582562 2151 O3 33284 Tylenchoidea G. pallida ERR202492
99.22 30583755 507 O2 33283 Tylenchomorpha G. pallida ERR202492
99.21 30578964 71917 F1 33286 Heteroderinae G. pallida ERR202492
0.74 228813 228813 U 0 unclassified G. pallida ERR202492
0.03 9354 252 D 2 Bacteria G. pallida ERR202492
0.02 5572 282 P 1224 Proteobacteria G. pallida ERR202492
0.01 1836 402 F 75682 Oxalobacteraceae G. pallida ERR202492
0.01 1942 115 C 1236 Gammaproteobacteria G. pallida ERR202492
0.01 2323 155 O 80840 Burkholderiales G. pallida ERR202492
0.01 2458 86 C 28216 Betaproteobacteria G. pallida ERR202492
Proportion of reads Reads rooted to taxon clade taxon-specific reads rank code Taxid Taxon Source Species SRA
85.23 26295871 631 O2 33283 Tylenchomorpha M. javanica ERR790020
85.18 26278729 985 O3 33284 Tylenchoidea M. javanica ERR790020
14.28 4404990 4404990 U 0 unclassified M. javanica ERR790020
0.45 138563 1002 D 2 Bacteria M. javanica ERR790020
0.26 78919 125 D1 1783272 Terrabacteria group M. javanica ERR790020
0.21 63936 55 P 1239 Firmicutes M. javanica ERR790020
0.14 43539 34 F 186817 Bacillaceae M. javanica ERR790020
0.13 39433 488 P 1224 Proteobacteria M. javanica ERR790020
0.12 36797 35836 G1 86661 Bacillus cereus group M. javanica ERR790020
0.12 37775 142 G 1386 Bacillus M. javanica ERR790020
0.09 27321 122 C 1236 Gammaproteobacteria M. javanica ERR790020
0.04 10990 83 C 1760 Actinobacteria M. javanica ERR790020
0.04 11634 11634 S 91844 Candidatus Portiera aleyrodidarum M. javanica ERR790020
0.03 8041 65 F1 33286 Heteroderinae M. javanica ERR790020
0.02 4727 24 O 91347 Enterobacterales M. javanica ERR790020
0.02 5469 5469 S 1570 Halobacillus halophilus M. javanica ERR790020
0.02 5554 22 F 49546 Flavobacteriaceae M. javanica ERR790020
0.02 5763 5763 S 51515 Dehalobacterium formicoaceticum M. javanica ERR790020
0.02 6065 67 G 1485 Clostridium M. javanica ERR790020
0.02 7553 7553 S1 331113 Simkania negevensis Z M. javanica ERR790020
0.01 1851 22 G 237 Flavobacterium M. javanica ERR790020
0.01 1903 22 F 85023 Microbacteriaceae M. javanica ERR790020
0.01 1994 16 P 1117 Cyanobacteria M. javanica ERR790020
0.01 2120 218 G 286 Pseudomonas M. javanica ERR790020
0.01 2191 2171 S 1747 Cutibacterium acnes M. javanica ERR790020
0.01 2198 2198 S 12253 Tomato mosaic virus M. javanica ERR790020
0.01 2278 24 G 1912216 Cutibacterium M. javanica ERR790020
0.01 2348 26 F 31957 Propionibacteriaceae M. javanica ERR790020
0.01 2405 2405 S1 1874362 Campylobacter pinnipediorum subsp. caledonicus M. javanica ERR790020
0.01 2487 2487 S 646637 Streptomyces sp. M2 M. javanica ERR790020
0.01 2543 173 G 469 Acinetobacter M. javanica ERR790020
0.01 2550 397 G 1301 Streptococcus M. javanica ERR790020
0.01 2692 11 G 194 Campylobacter M. javanica ERR790020
0.01 2692 2692 S 1492 Clostridium butyricum M. javanica ERR790020
0.01 2840 11 O 80840 Burkholderiales M. javanica ERR790020
0.01 2901 15 C 28211 Alphaproteobacteria M. javanica ERR790020
0.01 3450 634 F 543 Enterobacteriaceae M. javanica ERR790020
0.01 3859 11 O 186826 Lactobacillales M. javanica ERR790020
0.01 4358 179 G 1883 Streptomyces M. javanica ERR790020
Proportion of reads Reads rooted to taxon clade taxon-specific reads rank code Taxid Taxon Source Species SRA
83.62 30208155 623 O2 33283 Tylenchomorpha M. arenaria ERR790021
83.59 30200098 1194 O3 33284 Tylenchoidea M. arenaria ERR790021
15.86 5729345 5729345 U 0 unclassified M. arenaria ERR790021
0.49 175784 796 D 2 Bacteria M. arenaria ERR790021
0.31 111238 154 D1 1783272 Terrabacteria group M. arenaria ERR790021
0.22 78559 50 P 1239 Firmicutes M. arenaria ERR790021
0.18 65256 13 C 91061 Bacilli M. arenaria ERR790021
0.17 60002 11 O 1385 Bacillales M. arenaria ERR790021
0.15 53041 88 F 186817 Bacillaceae M. arenaria ERR790021
0.14 49114 187 G 1386 Bacillus M. arenaria ERR790021
0.13 47856 45296 G1 86661 Bacillus cereus group M. arenaria ERR790021
0.1 35545 892 P 1224 Proteobacteria M. arenaria ERR790021
0.08 28005 91 C 1760 Actinobacteria M. arenaria ERR790021
0.05 16321 118 F 31957 Propionibacteriaceae M. arenaria ERR790021
0.04 14709 141 C 1236 Gammaproteobacteria M. arenaria ERR790021
0.04 15264 14533 S 1747 Cutibacterium acnes M. arenaria ERR790021
0.04 16033 104 G 1912216 Cutibacterium M. arenaria ERR790021
0.03 11344 74 F1 33286 Heteroderinae M. arenaria ERR790021
0.02 5597 5597 S 2029983 Chitinophaga caeni M. arenaria ERR790021
0.02 5865 5865 S1 331113 Simkania negevensis Z M. arenaria ERR790021
0.02 7082 283 G 1485 Clostridium M. arenaria ERR790021
0.02 7943 18 F 49546 Flavobacteriaceae M. arenaria ERR790021
0.02 8846 39 C 28211 Alphaproteobacteria M. arenaria ERR790021
0.01 1916 1916 S 1536774 Paenibacillus sp. FSL H7-0357 M. arenaria ERR790021
0.01 1935 184 G 286 Pseudomonas M. arenaria ERR790021
0.01 1963 16 O 85007 Corynebacteriales M. arenaria ERR790021
0.01 2029 18 O 135622 Alteromonadales M. arenaria ERR790021
0.01 2069 2069 S 1678728 Flavobacterium kingsejongi M. arenaria ERR790021
0.01 2280 15 O 80840 Burkholderiales M. arenaria ERR790021
0.01 2349 19 G 44249 Paenibacillus M. arenaria ERR790021
0.01 2568 2568 S 1492 Clostridium butyricum M. arenaria ERR790021
0.01 2618 51 G 237 Flavobacterium M. arenaria ERR790021
0.01 2973 2973 S 51515 Dehalobacterium formicoaceticum M. arenaria ERR790021
0.01 3041 455 F 543 Enterobacteriaceae M. arenaria ERR790021
0.01 3132 104 G 1279 Staphylococcus M. arenaria ERR790021
0.01 3340 3340 S 1570 Halobacillus halophilus M. arenaria ERR790021
0.01 3458 598 G 1301 Streptococcus M. arenaria ERR790021
0.01 3538 3538 S 2268461 Microbacterium sp. ABRD_28 M. arenaria ERR790021
0.01 3692 26 G 33882 Microbacterium M. arenaria ERR790021
0.01 3920 177 G 1883 Streptomyces M. arenaria ERR790021
0.01 4424 4424 S 2500532 Paracoccus sp. Arc7-R13 M. arenaria ERR790021
0.01 4699 4699 S1 1874362 Campylobacter pinnipediorum subsp. caledonicus M. arenaria ERR790021
0.01 4746 29 G 265 Paracoccus M. arenaria ERR790021
0.01 5058 35 O 91347 Enterobacterales M. arenaria ERR790021
0.01 5197 29 F 31989 Rhodobacteraceae M. arenaria ERR790021
0.01 5360 19 G 194 Campylobacter M. arenaria ERR790021
Proportion of reads Reads rooted to taxon clade taxon-specific reads rank code Taxid Taxon Source Species SRA
70.18 38275890 323730 O2 33283 Tylenchomorpha G. pallida SRR2389452
69.28 37787560 542522 O3 33284 Tylenchoidea G. pallida SRR2389452
28.39 15481907 15481907 U 0 unclassified G. pallida SRR2389452
1.42 774660 19941 F1 33286 Heteroderinae G. pallida SRR2389452
1.17 636686 27777 D 2 Bacteria G. pallida SRR2389452
0.79 428302 20022 P 1224 Proteobacteria G. pallida SRR2389452
0.4 220524 34307 C 28216 Betaproteobacteria G. pallida SRR2389452
0.27 146239 22120 O 80840 Burkholderiales G. pallida SRR2389452
0.18 97552 8903 C 28211 Alphaproteobacteria G. pallida SRR2389452
0.16 87901 1832 D1 1783272 Terrabacteria group G. pallida SRR2389452
0.15 80414 5058 P 976 Bacteroidetes G. pallida SRR2389452
0.15 81131 165 D2 68336 Bacteroidetes/Chlorobi group G. pallida SRR2389452
0.15 81358 12 D1 1783270 FCB group G. pallida SRR2389452
0.15 81832 7179 C 1236 Gammaproteobacteria G. pallida SRR2389452
0.1 54704 20943 F 75682 Oxalobacteraceae G. pallida SRR2389452
0.09 48210 652 P 1239 Firmicutes G. pallida SRR2389452
0.05 25469 987 O 204457 Sphingomonadales G. pallida SRR2389452
0.05 25978 2756 F 41295 Rhodospirillaceae G. pallida SRR2389452
0.05 28012 439 C 91061 Bacilli G. pallida SRR2389452
0.05 28082 279 O 72274 Pseudomonadales G. pallida SRR2389452
0.05 28199 827 O 204441 Rhodospirillales G. pallida SRR2389452
0.05 29673 10207 F 80864 Comamonadaceae G. pallida SRR2389452
0.04 20115 20115 S 1922225 Erythrobacter sp. Alg231-14 G. pallida SRR2389452
0.04 20368 54 G 1041 Erythrobacter G. pallida SRR2389452
0.04 20590 570 O 1385 Bacillales G. pallida SRR2389452
0.04 20893 5580 F 119060 Burkholderiaceae G. pallida SRR2389452
0.04 20936 187 F 335929 Erythrobacteraceae G. pallida SRR2389452
0.04 21140 4897 F 49546 Flavobacteriaceae G. pallida SRR2389452
0.04 22234 456 O 200644 Flavobacteriales G. pallida SRR2389452
0.04 22653 3727 O 206351 Neisseriales G. pallida SRR2389452
0.04 23270 1926 C 1760 Actinobacteria G. pallida SRR2389452
0.04 24528 204 P 201174 Actinobacteria G. pallida SRR2389452
0.03 13690 2029 F 76892 Caulobacteraceae G. pallida SRR2389452
0.03 13981 215 F 186817 Bacillaceae G. pallida SRR2389452
0.03 14763 2006 O 356 Rhizobiales G. pallida SRR2389452
0.03 15303 1910 O 768507 Cytophagales G. pallida SRR2389452
0.03 15341 8994 G 469 Acinetobacter G. pallida SRR2389452
0.03 16420 3898 F 563835 Chitinophagaceae G. pallida SRR2389452
0.03 16735 188 O 186802 Clostridiales G. pallida SRR2389452
0.03 16854 5100 F 1499392 Chromobacteriaceae G. pallida SRR2389452
0.03 16899 2661 F 84566 Sphingobacteriaceae G. pallida SRR2389452
0.03 17540 77 C 186801 Clostridia G. pallida SRR2389452
0.03 17545 1221 F 468 Moraxellaceae G. pallida SRR2389452
0.03 18205 13606 G 191 Azospirillum G. pallida SRR2389452
0.03 18569 8142 G 149698 Massilia G. pallida SRR2389452
0.02 10258 574 F 135621 Pseudomonadaceae G. pallida SRR2389452
0.02 10859 1220 O 206389 Rhodocyclales G. pallida SRR2389452
0.02 11013 5039 O2 224471 Burkholderiales Genera incertae sedis G. pallida SRR2389452
0.02 11580 1633 G 1386 Bacillus G. pallida SRR2389452
0.02 11637 7961 G 963 Herbaspirillum G. pallida SRR2389452
0.02 13397 1273 O 91347 Enterobacterales G. pallida SRR2389452
0.02 13575 1982 O1 119065 unclassified Burkholderiales G. pallida SRR2389452
0.02 8205 2436 G 79328 Chitinophaga G. pallida SRR2389452
0.02 8275 2424 F 543 Enterobacteriaceae G. pallida SRR2389452
0.02 8344 247 G 47420 Hydrogenophaga G. pallida SRR2389452
0.02 8960 292 F 89373 Cytophagaceae G. pallida SRR2389452
0.02 9593 2478 G 286 Pseudomonas G. pallida SRR2389452
0.01 2739 2739 S 29442 Pseudomonas tolaasii G. pallida SRR2389452
0.01 2860 1306 G 535 Chromobacterium G. pallida SRR2389452
0.01 2927 2414 G 75 Caulobacter G. pallida SRR2389452
0.01 3144 11 O 213849 Campylobacterales G. pallida SRR2389452
0.01 3159 578 F 31989 Rhodobacteraceae G. pallida SRR2389452
0.01 3177 3153 S 48296 Acinetobacter pittii G. pallida SRR2389452
0.01 3191 11 C 29547 Epsilonproteobacteria G. pallida SRR2389452
0.01 3210 3210 S 1678028 Massilia sp. NR 4-1 G. pallida SRR2389452
0.01 3282 48 G1 136843 Pseudomonas fluorescens group G. pallida SRR2389452
0.01 3315 292 O 171549 Bacteroidales G. pallida SRR2389452
0.01 3324 773 F1 227290 Rhizobium/Agrobacterium group G. pallida SRR2389452
0.01 3336 830 F 85023 Microbacteriaceae G. pallida SRR2389452
0.01 3496 13 O 204455 Rhodobacterales G. pallida SRR2389452
0.01 3546 676 F 41297 Sphingomonadaceae G. pallida SRR2389452
0.01 3857 29 G1 909768 Acinetobacter calcoaceticus/baumannii complex G. pallida SRR2389452
0.01 3858 54 C 31969 Mollicutes G. pallida SRR2389452
0.01 3916 22 C 200643 Bacteroidia G. pallida SRR2389452
0.01 3973 2523 S 1491 Clostridium botulinum G. pallida SRR2389452
0.01 4050 859 G 1883 Streptomyces G. pallida SRR2389452
0.01 4127 198 O 85007 Corynebacteriales G. pallida SRR2389452
0.01 4207 205 C 28221 Deltaproteobacteria G. pallida SRR2389452
0.01 4317 89 F 2062 Streptomycetaceae G. pallida SRR2389452
0.01 4447 88 O 135622 Alteromonadales G. pallida SRR2389452
0.01 4482 468 F 32033 Xanthomonadaceae G. pallida SRR2389452
0.01 4513 491 F 82115 Rhizobiaceae G. pallida SRR2389452
0.01 4549 1675 G 237 Flavobacterium G. pallida SRR2389452
0.01 4708 4708 S1 485918 Chitinophaga pinensis DSM 2588 G. pallida SRR2389452
0.01 4908 615 F 506 Alcaligenaceae G. pallida SRR2389452
0.01 5028 3677 G 28453 Sphingobacterium G. pallida SRR2389452
0.01 5058 5058 S1 526973 Bacillus cereus m1293 G. pallida SRR2389452
0.01 5225 245 O 32003 Nitrosomonadales G. pallida SRR2389452
0.01 5504 5504 S 2306583 Halomonas sp. JS92-SW72 G. pallida SRR2389452
0.01 5559 5559 S 1677857 Hungateiclostridium saccincola G. pallida SRR2389452
0.01 5705 3302 G 59732 Chryseobacterium G. pallida SRR2389452
0.01 5826 5826 S 748280 Pseudogulbenkiania sp. NH8B G. pallida SRR2389452
0.01 5860 269 O 135614 Xanthomonadales G. pallida SRR2389452
0.01 6030 3679 G 73029 Dechloromonas G. pallida SRR2389452
0.01 6163 349 S 1396 Bacillus cereus G. pallida SRR2389452
0.01 6184 2141 G 32008 Burkholderia G. pallida SRR2389452
0.01 6481 715 G 2745 Halomonas G. pallida SRR2389452
0.01 6785 40 F 28256 Halomonadaceae G. pallida SRR2389452
0.01 6983 510 O 186826 Lactobacillales G. pallida SRR2389452
0.01 7050 305 G1 86661 Bacillus cereus group G. pallida SRR2389452
0.01 7260 1093 P 1117 Cyanobacteria G. pallida SRR2389452
0.01 7272 1510 O 85006 Micrococcales G. pallida SRR2389452
0.01 7285 2691 G 423349 Mucilaginibacter G. pallida SRR2389452
0.01 7572 66 O 135619 Oceanospirillales G. pallida SRR2389452
0.01 7650 7512 S 78587 Asticcacaulis excentricus G. pallida SRR2389452
0.01 7772 7772 S 2184519 Hydrogenophaga sp. NH-16 G. pallida SRR2389452
0.01 7823 678 G 1485 Clostridium G. pallida SRR2389452
0.01 8050 25 F 31979 Clostridiaceae G. pallida SRR2389452
Proportion of reads Reads rooted to taxon clade taxon-specific reads rank code Taxid Taxon Source Species SRA
93.97 28073787 1899 O2 33283 Tylenchomorpha G. ellingtonae SRR3162514
93.95 28070030 7449 O3 33284 Tylenchoidea G. ellingtonae SRR3162514
93.91 28057567 40650 F1 33286 Heteroderinae G. ellingtonae SRR3162514
4.99 1491074 1491074 U 0 unclassified G. ellingtonae SRR3162514
0.13 39802 1626 D 2 Bacteria G. ellingtonae SRR3162514
0.1 28497 20210 P 1224 Proteobacteria G. ellingtonae SRR3162514
0.03 7472 30 D1 1783272 Terrabacteria group G. ellingtonae SRR3162514
0.02 4515 103 C 1236 Gammaproteobacteria G. ellingtonae SRR3162514
0.01 1708 30 P 976 Bacteroidetes G. ellingtonae SRR3162514
0.01 1825 1825 S2 1365647 Xanthomonas euvesicatoria pv. alfalfae CFBP 3836 G. ellingtonae SRR3162514
0.01 1915 22 O 1385 Bacillales G. ellingtonae SRR3162514
0.01 1954 1954 S1 1200984 Streptomyces lividans 1326 G. ellingtonae SRR3162514
0.01 1989 60 C 28211 Alphaproteobacteria G. ellingtonae SRR3162514
0.01 2194 72 G 1883 Streptomyces G. ellingtonae SRR3162514
0.01 2338 11 C 91061 Bacilli G. ellingtonae SRR3162514
0.01 3255 18 P 1239 Firmicutes G. ellingtonae SRR3162514
0.01 3462 90 C 1760 Actinobacteria G. ellingtonae SRR3162514
Proportion of reads Reads rooted to taxon clade taxon-specific reads rank code Taxid Taxon Source Species SRA
93.3 10730672 79467 O2 33283 Tylenchomorpha H. glycines SRR6269844
92.54 10642968 66339 O3 33284 Tylenchoidea H. glycines SRR6269844
90.73 10434857 1014172 F1 33286 Heteroderinae H. glycines SRR6269844
5.26 605129 341864 D 2 Bacteria H. glycines SRR6269844
1.28 147037 147037 U 0 unclassified H. glycines SRR6269844
1.15 131998 64497 P 1224 Proteobacteria H. glycines SRR6269844
1.09 125245 67 D1 1783272 Terrabacteria group H. glycines SRR6269844
1.08 123897 41 P 1239 Firmicutes H. glycines SRR6269844
1.07 122930 17 O 1385 Bacillales H. glycines SRR6269844
1.07 123180 11 C 91061 Bacilli H. glycines SRR6269844
0.81 93587 2453 G 1279 Staphylococcus H. glycines SRR6269844
0.79 90934 90934 S 1286 Staphylococcus simulans H. glycines SRR6269844
0.35 40388 779 C 28216 Betaproteobacteria H. glycines SRR6269844
0.34 39339 1612 O 80840 Burkholderiales H. glycines SRR6269844
0.24 27634 27634 S1 526973 Bacillus cereus m1293 H. glycines SRR6269844
0.24 27679 36 S 1396 Bacillus cereus H. glycines SRR6269844
0.24 27741 29 G1 86661 Bacillus cereus group H. glycines SRR6269844
0.24 27987 34 G 1386 Bacillus H. glycines SRR6269844
0.16 18542 80 C 1236 Gammaproteobacteria H. glycines SRR6269844
0.16 18658 1587 F 80864 Comamonadaceae H. glycines SRR6269844
0.14 15602 15602 S 2306583 Halomonas sp. JS92-SW72 H. glycines SRR6269844
0.12 14279 14279 S 2184519 Hydrogenophaga sp. NH-16 H. glycines SRR6269844
0.1 11137 859 O1 119065 unclassified Burkholderiales H. glycines SRR6269844
0.08 9457 3902 O2 224471 Burkholderiales Genera incertae sedis H. glycines SRR6269844
0.07 8145 182 C 28211 Alphaproteobacteria H. glycines SRR6269844
0.05 5199 27 P 976 Bacteroidetes H. glycines SRR6269844
0.05 5207 836 F 119060 Burkholderiaceae H. glycines SRR6269844
0.05 6321 6321 S 1034377 Soybean cyst nematode socyvirus H. glycines SRR6269844
0.03 3516 183 G 107 Spirosoma H. glycines SRR6269844
0.03 3678 17 O 768507 Cytophagales H. glycines SRR6269844
0.02 1853 1846 G1 114292 typhus group H. glycines SRR6269844
0.02 1897 12 G 780 Rickettsia H. glycines SRR6269844
0.02 2124 2124 S 2057025 Spirosoma pollinicola H. glycines SRR6269844
0.02 2281 2281 S1 395495 Leptothrix cholodnii SP-6 H. glycines SRR6269844
0.02 2408 2408 S 96344 Cupriavidus oxalaticus H. glycines SRR6269844
0.02 2586 312 F 41297 Sphingomonadaceae H. glycines SRR6269844
0.02 2592 641 F 75682 Oxalobacteraceae H. glycines SRR6269844
0.02 2873 226 O 204457 Sphingomonadales H. glycines SRR6269844
0.01 1002 262 G 44249 Paenibacillus H. glycines SRR6269844
0.01 1051 179 G 149698 Massilia H. glycines SRR6269844
0.01 1076 86 F 76892 Caulobacteraceae H. glycines SRR6269844
0.01 1191 80 F 186822 Paenibacillaceae H. glycines SRR6269844
0.01 1199 622 G 13687 Sphingomonas H. glycines SRR6269844
0.01 1255 95 O 356 Rhizobiales H. glycines SRR6269844
0.01 1332 53 G 286 Pseudomonas H. glycines SRR6269844
0.01 1631 1250 G 48736 Ralstonia H. glycines SRR6269844
0.01 1690 1690 S 1768242 Paucibacter sp. KCTC 42545 H. glycines SRR6269844
0.01 587 557 G 165695 Sphingobium H. glycines SRR6269844
0.01 669 122 G 20 Phenylobacterium H. glycines SRR6269844
0.01 684 684 S 1211326 Spirosoma aerolatum H. glycines SRR6269844
0.01 766 503 G 963 Herbaspirillum H. glycines SRR6269844
0.01 800 800 S 864051 Burkholderiales bacterium JOSHI_001 H. glycines SRR6269844
0.01 857 111 G 283 Comamonas H. glycines SRR6269844
0.01 881 881 S1 390235 Pseudomonas putida W619 H. glycines SRR6269844
Proportion of reads Reads rooted to taxon clade taxon-specific reads rank code Taxid Taxon Source Species SRA
92.88 11978072 122706 O2 33283 Tylenchomorpha H. glycines SRR6269845
91.8 11838666 96582 O3 33284 Tylenchoidea H. glycines SRR6269845
90.32 11648223 1223381 F1 33286 Heteroderinae H. glycines SRR6269845
6.04 778844 4308 D 2 Bacteria H. glycines SRR6269845
5.84 753772 6723 P 1224 Proteobacteria H. glycines SRR6269845
5.66 730524 1453 C 28216 Betaproteobacteria H. glycines SRR6269845
5.65 728391 1552 O 80840 Burkholderiales H. glycines SRR6269845
5.26 678448 267 F 119060 Burkholderiaceae H. glycines SRR6269845
5.25 677415 677415 S 96344 Cupriavidus oxalaticus H. glycines SRR6269845
5.25 677466 16 G 106589 Cupriavidus H. glycines SRR6269845
0.97 124856 124856 U 0 unclassified H. glycines SRR6269845
0.21 26534 1789 F 80864 Comamonadaceae H. glycines SRR6269845
0.17 22023 22023 S 2184519 Hydrogenophaga sp. NH-16 H. glycines SRR6269845
0.15 18854 2275 O1 119065 unclassified Burkholderiales H. glycines SRR6269845
0.13 16283 37 D1 1783272 Terrabacteria group H. glycines SRR6269845
0.12 15206 14 P 1239 Firmicutes H. glycines SRR6269845
0.12 15729 6855 O2 224471 Burkholderiales Genera incertae sedis H. glycines SRR6269845
0.11 14431 11 O 1385 Bacillales H. glycines SRR6269845
0.1 13146 40 C 1236 Gammaproteobacteria H. glycines SRR6269845
0.09 10992 10992 S 2306583 Halomonas sp. JS92-SW72 H. glycines SRR6269845
0.07 8400 14 G1 86661 Bacillus cereus group H. glycines SRR6269845
0.07 8529 8529 S 1034377 Soybean cyst nematode socyvirus H. glycines SRR6269845
0.07 8537 22 G 1386 Bacillus H. glycines SRR6269845
0.06 8344 8344 S1 526973 Bacillus cereus m1293 H. glycines SRR6269845
0.06 8375 27 S 1396 Bacillus cereus H. glycines SRR6269845
0.04 5426 5426 S 1286 Staphylococcus simulans H. glycines SRR6269845
0.04 5601 128 G 1279 Staphylococcus H. glycines SRR6269845
0.02 2203 656 G 149698 Massilia H. glycines SRR6269845
0.02 2341 2341 S 2057025 Spirosoma pollinicola H. glycines SRR6269845
0.02 2742 65 G 107 Spirosoma H. glycines SRR6269845
0.02 2787 2787 S1 395495 Leptothrix cholodnii SP-6 H. glycines SRR6269845
0.02 2825 231 C 28211 Alphaproteobacteria H. glycines SRR6269845
0.02 2836 271 F 75682 Oxalobacteraceae H. glycines SRR6269845
0.01 1742 1742 S 76731 Roseateles depolymerans H. glycines SRR6269845
0.01 1905 1905 S 1768242 Paucibacter sp. KCTC 42545 H. glycines SRR6269845
0.01 685 23 F 563835 Chitinophagaceae H. glycines SRR6269845
0.01 711 14 O 135614 Xanthomonadales H. glycines SRR6269845
0.01 764 764 S 1141883 Massilia putida H. glycines SRR6269845
0.01 776 308 G 12916 Acidovorax H. glycines SRR6269845
0.01 821 821 S 864051 Burkholderiales bacterium JOSHI_001 H. glycines SRR6269845
0.01 845 845 S1 983917 Rubrivivax gelatinosus IL144 H. glycines SRR6269845
0.01 865 88 O 356 Rhizobiales H. glycines SRR6269845
0.01 869 23 C 1760 Actinobacteria H. glycines SRR6269845
0.01 933 128 G 283 Comamonas H. glycines SRR6269845
Proportion of reads Reads rooted to taxon clade taxon-specific reads rank code Taxid Taxon Source Species SRA
95.93 5053142 5435 O3 33284 Tylenchoidea G. pallida SRR7775195
95.93 5053190 28 O2 33283 Tylenchomorpha G. pallida SRR7775195
95.81 5047167 24809 F1 33286 Heteroderinae G. pallida SRR7775195
1.82 95964 4043 D 2 Bacteria G. pallida SRR7775195
1.6 84529 9226 P 1224 Proteobacteria G. pallida SRR7775195
1.28 67199 7378 C 28216 Betaproteobacteria G. pallida SRR7775195
1.13 59594 18847 O 80840 Burkholderiales G. pallida SRR7775195
0.52 27242 11208 G 149698 Massilia G. pallida SRR7775195
0.52 27637 377 F 75682 Oxalobacteraceae G. pallida SRR7775195
0.29 15476 15476 S 1141883 Massilia putida G. pallida SRR7775195
0.23 11998 9765 F 119060 Burkholderiaceae G. pallida SRR7775195
0.14 7198 32 D1 1783272 Terrabacteria group G. pallida SRR7775195
0.13 7033 119 P 1239 Firmicutes G. pallida SRR7775195
0.12 6531 6531 U 0 unclassified G. pallida SRR7775195
0.1 5066 234 C 1236 Gammaproteobacteria G. pallida SRR7775195
0.1 5300 5300 S1 1239783 Bacillus atrophaeus UCMB-5137 G. pallida SRR7775195
0.05 2746 2746 S 2306583 Halomonas sp. JS92-SW72 G. pallida SRR7775195
0.05 2892 48 C 28211 Alphaproteobacteria G. pallida SRR7775195
0.04 1927 1927 S 1553431 Mycoavidus cysteinexigens G. pallida SRR7775195
0.03 1497 1443 F 135621 Pseudomonadaceae G. pallida SRR7775195
0.03 1538 1538 S 189426 Paenibacillus odorifer G. pallida SRR7775195
0.03 1753 365 F 41297 Sphingomonadaceae G. pallida SRR7775195
0.02 1009 1008 G 165697 Sphingopyxis G. pallida SRR7775195
0.02 819 271 F 80864 Comamonadaceae G. pallida SRR7775195
0.01 270 267 F 942 Anaplasmataceae G. pallida SRR7775195
0.01 375 375 G 13687 Sphingomonas G. pallida SRR7775195
0.01 375 375 G 41275 Brevundimonas G. pallida SRR7775195
0.01 498 498 S1 365046 Ramlibacter tataouinensis TTB310 G. pallida SRR7775195
0.01 527 527 S 1707785 Massilia sp. WG5 G. pallida SRR7775195
Proportion of reads Reads rooted to taxon clade taxon-specific reads rank code Taxid Taxon Source Species SRA
74.57 38244277 20662 O2 33283 Tylenchomorpha D.destructor SRR7943144
24.67 12650916 12650916 U 0 unclassified D.destructor SRR7943144
0.74 377285 24363 D 2 Bacteria D.destructor SRR7943144
0.43 222510 1353 D1 1783272 Terrabacteria group D.destructor SRR7943144
0.38 195024 169 P 1239 Firmicutes D.destructor SRR7943144
0.36 186199 118 C 91061 Bacilli D.destructor SRR7943144
0.35 178437 200 O 1385 Bacillales D.destructor SRR7943144
0.34 173238 124 G 1386 Bacillus D.destructor SRR7943144
0.34 174009 11 F 186817 Bacillaceae D.destructor SRR7943144
0.33 170904 170904 S1 526973 Bacillus cereus m1293 D.destructor SRR7943144
0.33 171059 126 S 1396 Bacillus cereus D.destructor SRR7943144
0.33 171332 106 G1 86661 Bacillus cereus group D.destructor SRR7943144
0.26 131538 13212 O3 33284 Tylenchoidea D.destructor SRR7943144
0.16 79642 3521 P 1224 Proteobacteria D.destructor SRR7943144
0.11 54016 14890 F1 33286 Heteroderinae D.destructor SRR7943144
0.09 44143 19 D2 68336 Bacteroidetes/Chlorobi group D.destructor SRR7943144
0.08 42879 562 P 976 Bacteroidetes D.destructor SRR7943144
0.07 36733 2516 C 1236 Gammaproteobacteria D.destructor SRR7943144
0.05 24443 24443 S 2057025 Spirosoma pollinicola D.destructor SRR7943144
0.05 25159 382 F 89373 Cytophagaceae D.destructor SRR7943144
0.04 21330 1063 C 28211 Alphaproteobacteria D.destructor SRR7943144
0.03 14857 480 C 1760 Actinobacteria D.destructor SRR7943144
0.02 10869 64 O 356 Rhizobiales D.destructor SRR7943144
0.02 8008 226 P 1117 Cyanobacteria D.destructor SRR7943144
0.02 8378 298 F 49546 Flavobacteriaceae D.destructor SRR7943144
0.02 8457 16 O 200644 Flavobacteriales D.destructor SRR7943144
0.02 9563 323 C 28216 Betaproteobacteria D.destructor SRR7943144
0.01 2627 2627 S1 224013 Nostoc piscinale CENA21 D.destructor SRR7943144
0.01 2749 2749 S 95300 Pseudomonas vancouverensis D.destructor SRR7943144
0.01 2820 2820 S 2004644 Acinetobacter sp. WCHA45 D.destructor SRR7943144
0.01 2847 2847 S 1813019 Campylobacter hepaticus D.destructor SRR7943144
0.01 2866 29 G 1177 Nostoc D.destructor SRR7943144
0.01 2937 845 G 1883 Streptomyces D.destructor SRR7943144
0.01 3020 3020 S 2014542 Alcanivorax sp. N3-2A D.destructor SRR7943144
0.01 3057 17 G 59753 Alcanivorax D.destructor SRR7943144
0.01 3103 1014 G 662 Vibrio D.destructor SRR7943144
0.01 3415 224 F 641 Vibrionaceae D.destructor SRR7943144
0.01 3667 14 F 171552 Prevotellaceae D.destructor SRR7943144
0.01 3716 57 O 1161 Nostocales D.destructor SRR7943144
0.01 3804 3792 S 1491 Clostridium botulinum D.destructor SRR7943144
0.01 4261 17 O 171549 Bacteroidales D.destructor SRR7943144
0.01 4373 84 G 194 Campylobacter D.destructor SRR7943144
0.01 4496 142 G 469 Acinetobacter D.destructor SRR7943144
0.01 4761 29 G 1485 Clostridium D.destructor SRR7943144
0.01 4800 14 F 31979 Clostridiaceae D.destructor SRR7943144
0.01 4813 909 F 119060 Burkholderiaceae D.destructor SRR7943144
0.01 4880 18 F 2062 Streptomycetaceae D.destructor SRR7943144
0.01 5080 5080 S1 316058 Rhodopseudomonas palustris HaA2 D.destructor SRR7943144
0.01 5879 746 G 286 Pseudomonas D.destructor SRR7943144
0.01 6121 36 F 135621 Pseudomonadaceae D.destructor SRR7943144
0.01 6586 59 O 80840 Burkholderiales D.destructor SRR7943144
0.01 6918 571 O 91347 Enterobacterales D.destructor SRR7943144
0.01 6952 22 O 186802 Clostridiales D.destructor SRR7943144
0.01 7644 149 O 186826 Lactobacillales D.destructor SRR7943144

Kraken Large green hexagons are the source species RNASEQ, red diamonds are viruses, and triangles are bacteria present in two or more species.

Sources

The best source to get more information on kraken2

https://github.com/DerrickWood/kraken2/blob/master/docs/MANUAL.markdown

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