Questions tagged [seqkit]

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2 votes
2 answers

How do I save selected sequences in seqkit to a file?

Consider: seqkit grep -nrp ";s__nosocomialis;" ribogrove_11.217_sequences.fasta Using this command lets me select all sequences related to the organism "A. nosocomialis" in the ...
Freezing Soul's user avatar
3 votes
3 answers

How to get strain names/ids contained in a multi FASTA file using seqkit?

FASTA files can be very big and unwieldy, especially if lines are at most 80 characters, one can't speed up browsing them by using less with ...
Cornelius Roemer's user avatar
1 vote
2 answers

Checking that two multiline FASTAs are identical (allowing for different order and lower/upper case)

Is there a good CLI tool that can diff two multiline fasta files, ignoring order, and comparing sequences with identical names with each other pairwise. Bonus points if lower/upper case is tolerated (...
Cornelius Roemer's user avatar