Extract and filter

The seqkit seq command is used to extract, filter and format your FASTA and FASTQ files.

For example, to extract the sequence names from a FASTA file:

If your FASTA is formatted such that the sequence name contains an ID followed by a space and more information, then you can extract just those IDs using --only-id:

If you are interested in only sequences of a certain size, e.g. >300bp, use the --min-len to filter out shorter sequences:

You can also filter out long sequences with --max-len, and for FASTQ files, you can filter out reads with a certain average quality with --min-qual and --max-qual.