Converting FASTQ format to FASTA

There are several ways you can convert fastq to fasta sequences. Some methods are listed below.

Using SED

sed can be used to selectively print the desired lines from a file, so if you print the first and 2rd line of every 4 lines, you get the sequence header and sequence needed for fasta format.

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sed -n '1~4s/^@/>/p;2~4p' INFILE.fastq > OUTFILE.fasta

Using PASTE

You can linerize every 4 lines in a tabular format and print first and second field using paste

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cat INFILE.fastq | paste - - - - |cut -f 1, 2| sed 's/@/>/'g | tr -s "/t" "/n" > OUTFILE.fasta

EMBOSS:seqret

Standard script that can be used for many purposes. One such use is fastq-fasta conversion

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seqret -sequence reads.fastq -outseq reads.fasta

awk can be used for conversion as follows:

Using AWK

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cat infile.fq | awk '{if(NR%4==1) {printf(">%s\n",substr($0,2));} else if(NR%4==2) print;}' > file.fa

FASTX-toolkit

fastq_to_fasta is available in the FASTX-toolkit that scales really well with the huge datasets

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fastq_to_fasta -h
usage: fastq_to_fasta [-h] [-r] [-n] [-v] [-z] [-i INFILE] [-o OUTFILE]
# Remember to use -Q33 for illumina reads!
version 0.0.6
	   [-h]         = This helpful help screen.
	   [-r]         = Rename sequence identifiers to numbers.
	   [-n]         = keep sequences with unknown (N) nucleotides.
			       Default is to discard such sequences.
	   [-v]         = Verbose - report number of sequences.
			       If [-o] is specified,  report will be printed to STDOUT.
			       If [-o] is not specified (and output goes to STDOUT),
			       report will be printed to STDERR.
	   [-z]         = Compress output with GZIP.
	   [-i INFILE]  = FASTA/Q input file. default is STDIN.
	   [-o OUTFILE] = FASTA output file. default is STDOUT.

Bioawk

Another option to convert fastq to fasta format using bioawk

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bioawk -c fastx '{print ">"$name"\n"$seq}' input.fastq > output.fasta

Seqtk

From the same developer, there is another option using a tool called seqtk

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seqtk seq -a input.fastq > output.fasta

Note that you can use either compressed or uncompressed files for this tool

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