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Feature request: output .fna file of reads (not) matching the database #14

Closed colinbrislawn closed 3 years ago

colinbrislawn commented 4 years ago

Some aligners are able to output the query reads that do (or do not) match to the database.

bbduk.sh outm=hits.fna out=misses.fna vsearch --matched hits.fna --notmatched misses.fna

I think this would be a convenient feature for magic-blast. ⚡️

Thanks for making a new splice-aware aligner!

boratyng commented 4 years ago

Thank you for using Magic-BLAST and for your suggestion. We plan to add this feature in a future release.

At this point we have -no_unaligned option, if you are only interested in reads that align to your target.

y9c commented 3 years ago

Hi @colinbrislawn, There is a -out_unaligned argument for this in version 1.6.0 now.

boratyng commented 3 years ago

Additionally, you can use -unaligned_fmt option to select output format for unaligned reads. Choices are: SAM, tabular, and FASTA formats. The same format as for aligned reads is used by default.