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