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

seqtk 1.0                                         February 2014                                         SEQTK(1)