Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. It seamlessly parses both FASTA and FASTQ files which can also be optionally compressed by gzip.
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Convert FASTQ to FASTA:
seqtk seq -a in.fq.gz > out.fa -
Convert ILLUMINA 1.3+ FASTQ to FASTA and mask bases with quality lower than 20 to lowercases (the 1st command line) or to
N(the 2nd):seqtk seq -aQ64 -q20 in.fq > out.fa seqtk seq -aQ64 -q20 -n N in.fq > out.fa -
Fold long FASTA/Q lines and remove FASTA/Q comments:
seqtk seq -Cl60 in.fa > out.fa -
Convert multi-line FASTQ to 4-line FASTQ:
seqtk seq -l0 in.fq > out.fq -
Reverse complement FASTA/Q:
seqtk seq -r in.fq > out.fq -
Extract sequences with names in file
name.lst, one sequence name per line:seqtk subseq in.fq name.lst > out.fq -
Extract sequences in regions contained in file
reg.bed:seqtk subseq in.fa reg.bed > out.fa -
Mask regions in
reg.bedto lowercases:seqtk seq -M reg.bed in.fa > out.fa -
Subsample 10000 read pairs from two large paired FASTQ files (remember to use the same random seed to keep pairing):
seqtk sample -s100 read1.fq 10000 > sub1.fq seqtk sample -s100 read2.fq 10000 > sub2.fq -
Trim low-quality bases from both ends using the Phred algorithm:
seqtk trimfq in.fq > out.fq -
Trim 5bp from the left end of each read and 10bp from the right end:
seqtk trimfq -b 5 -e 10 in.fa > out.fa