Man page - seqtk(1)

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Package:  seqtk
apt-get install seqtk

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• seqtk(1)
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• seqtk

Manual

SEQTK

NAME
SYNOPSIS
DESCRIPTION
COMMANDS

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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

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