Introduction

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. To install seqtk,

git clone https://github.com/lh3/seqtk.git;
cd seqtk; make

The only library dependency is zlib.

Seqtk Examples

• 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.bed to 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
  

• Keep the 50bp from right end of each read by trimming the rest and if the trimmed read length ends up having less the 20bp then the first 20 bp should be kept only:

      seqtk trimfq -E 50 -s 20 in.fq > out.fq