bonito basecaller to have a resume mode

[Kirk3gaard]

Hi

It would be great if the bonito basecaller had a --resume mode in case something crashes or more reads are generated to avoid having to basecall everything from scratch or manually figure out which files have been basecalled.

Best regards Rasmus

[iiSeymour]

Hey @Kirk3gaard

You can use --skip --read-ids with the output redirection append operator >> to achieve this.

$ grep -Po '^>\K.*' calls.fasta > read-ids.txt
$ bonito basecaller dna_r9.4.1 --skip --read-ids read-ids.txt reads >> calls.fasta

Note: if providing a reference and outputting sam you'll want to use a new output file as appending will produce an invalid file.

[Kirk3gaard]

Hi Chris

Thanks. That is a nice workaround.

Best Rasmus