seqtk(1) 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