seqtk

seqtk <command> <arguments>

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.

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