NAME

       seqtk - sampling, trimming, fastq2fasta, subsequence, reverse complement

SYNOPSIS

       seqtk <command> <arguments>

DESCRIPTION

       Currently,  seqtk  supports  quality  based  trimming with the phred algorithm, converting
       fastq to fasta, reverse complementing sequences, extracting  or  masking  subsequences  in
       regions  given  in  a  BED/name  list file, and more.  It contains a subsampling module to
       sample exactly n sequences or a fraction of sequences.

       Seqtk supports both fasta and fastq input files, which can be optionally gzip compressed.

COMMANDS

       Command: seq       common transformation of FASTA/Q

       comp   get the nucleotide composition of FASTA/Q

       sample subsample sequences

       subseq extract subsequences from FASTA/Q

       trimfq trim FASTQ using the Phred algorithm

       hety   regional heterozygosity

       mutfa  point mutate FASTA at specified positions

       mergefa
              merge two FASTA/Q files

       randbase
              choose a random base from hets

       cutN   cut sequence at long N

       listhet
              extract the position of each het