Andrew Severin

Andrew Severin

His PhD was in Biophysics/NMR spectroscopy. He did a Bioinformatics Postdoc in Soybean genetics and now runs the Genome Informatics Facility at Iowa State University. He is passionate about evolution and the science behind the genome. There is so much we don't know about how the elements in a genome interact to create the fine balance of gene expression, modification and 3D structure that create the dynamic range of phenotypes we observe. As sequencing technology continues to improve and the cost continues to decrease, we will be able to ask more complex questions that increase our understanding via comparative and translational genomics.

Background

This particular genome is interesting because it shows insecticidal activity against Diptera. The raw data contains 1.5G of data and the genome size is 6.4 mb. Here is more background reading.

ENA Files

SeqType Platform BioProject Experiment Files    
short Reads Illumina HiSeq 2000 PRJNA288953 Bacillus thuringiensis strain:HS18-1 Genome sequencing and assembly Forward1 Reverse2  
short Reads Illumina HiSeq 2000 PRJNA288953 Bacillus thuringiensis strain:HS18-1 Genome sequencing and assembly Forward1 Reverse2  
Long Reads PacBio RS II PRJNA288953 Bacillus thuringiensis strain:HS18-1 Genome sequencing and assembly PacbioReads    

How to download the data from ENA

The European Nucleotide Archive has the files already in fastq format and it is easy to download. The main page with this project data is PRJNA288953 We are only going to take the pacbio data which is the 3rd file link under the ‘'’Read Files’’’ tab.

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wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR209/001/SRR2093871/SRR2093871_1.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR209/001/SRR2093871/SRR2093871_2.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR209/002/SRR2093872/SRR2093872_1.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR209/002/SRR2093872/SRR2093872_2.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR209/006/SRR2093876/SRR2093876_subreads.fastq.gz

SRA files

Run Instrument Layout Insert (bp) ReadLength TotalReads Bases (Mbp)
SRR2093876 PacBio RS II Single read 0 2563   1398
SRR2093871 Illumina HiSeq 2000 paired-end 200 100x2   1,339
SRR2093872 Illumina HiSeq 2000 mate-pair 2000 100x2   1,405

How to download from SRA

Downloading from SRA will be performed using the sra-toolkit. Additional metadata for these files can be found on NCBI here: SAMN03840349

  • create a file with the SRA ids and name it srr.ids

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    SRR2093872
SRR2093871
  • Assuming the sra-toolkit is installed then load the module and run the following bash script on the command line. 
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    module load sra-toolkit
while read line; do
  fastq-dump --split-files --origfmt ${line};
done<srr.ids
  • The pacbio data has to be downloaded separately 
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      fastq-dump --table SEQUENCE --origfmt SRR2093876

Assembly statistics for Bacillus thuringiensis

This assembly will be considered the gold standard that we strive for with the different assembly programs.

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---------------- Information for assembly 'GCA_001182785.1_ASM118278v1_genomic.fna' ----------------


                                         Number of scaffolds         10
                                     Total size of scaffolds    6403459
                                            Longest scaffold    5292526
                                           Shortest scaffold       4669
                                 Number of scaffolds > 1K nt         10 100.0%
                                Number of scaffolds > 10K nt          7  70.0%
                               Number of scaffolds > 100K nt          3  30.0%
                                 Number of scaffolds > 1M nt          1  10.0%
                                Number of scaffolds > 10M nt          0   0.0%
                                          Mean scaffold size     640346
                                        Median scaffold size      92085
                                         N50 scaffold length    5292526
                                          L50 scaffold count          1
                                                 scaffold %A      32.55
                                                 scaffold %C      17.46
                                                 scaffold %G      17.54
                                                 scaffold %T      32.44
                                                 scaffold %N       0.00
                                         scaffold %non-ACGTN       0.00
                             Number of scaffold non-ACGTN nt          0