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