SEQTK(1)

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