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hsinnan75 / MapCaller

MapCaller – An efficient and versatile approach for short-read alignment and variant detection in high-throughput sequenced genomes
MIT License
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Automatic index of a FASTA file reference #48

Closed tseemann closed 4 years ago

tseemann commented 4 years ago

For bacterial genomes it is very fast to bwt_index and we do it on every analysis because the references change all the time, but we do not want lots of temporary files.

Would it be possible to accept a FASTA file reference directly (for -i or a new option) and automatically index it, preferably keep in RAM only, or use temporary folder eg /tmp or /dev/shm for speed. And then delete the files at the end?

To be able to do this would make it much easier for bacterial genome analysis!

% MapCaller -ref reference.fasta -f R1.fq -f2 R2.fq ....
hsinnan75 commented 4 years ago

Thanks for the suggestion. I'll add this feature to MapCaller.

hsinnan75 commented 4 years ago

I've updated MapCaller to v0.9.9.28. It builds the bwt index files on the fly. The built index files will be removed after the job is done.

% MapCaller -r reference.fasta -f R1.fq -f2 R2.fq ....

tseemann commented 4 years ago

This is very helpful !