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.

• 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