SYNOPSISseqtk <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.
COMMANDSCommand: seq common transformation of FASTA/Q
- get the nucleotide composition of FASTA/Q
- subsample sequences
- extract subsequences from FASTA/Q
- trim FASTQ using the Phred algorithm
- regional heterozygosity
- point mutate FASTA at specified positions
- merge two FASTA/Q files
- choose a random base from hets
- cut sequence at long N
extract the position of each het