Benjamin Buchfink comments

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                                            Benjamin Buchfink

Question about diamondpy

The project was not formally created or endorsed by me, although I guess it's ok to use it.

Unrecognized sequence character in BLAST database

I tested this with the latest nr database and could not reproduce the error. Maybe it was fixed by now by NCBI?

Create multi-platform Docker image on release

now providing multi-platform docker image

Create multi-platform Docker image on release

fixed the tag issue

DIAMOND blastx extremely slow during "Computing alignments..." stage

Diamond is not well adapted to very long queries of several megabases. You can try frameshift alignment mode, e.g. `-F 15 --range-culling --top 10`. (worth a try, but will not...

ERROR [diamond_search()]

This does not look like a diamond error. Please ask the downstream provider (SonicParanoid) for support.

paired-end diamond with local database

Yes you can, you just need to be aware that diamond will always treat the reads separately.

`--soft-masking` does not accept documented value `none` and `seg`

Thanks, it will be fixed in the next release.

Request: pre-built databases for download

Diamond now fully supports BLAST databases, including taxonomy. https://ftp.ncbi.nlm.nih.gov/blast/db/

`--swipe` not producing any output

Thanks, it will be fixed in the next release. Fine to use an older version until then.