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immcantation / presto

pRESTO is part of the Immcantation analysis framework for Adaptive Immune Receptor Repertoire sequencing (AIRR-seq). pRESTO is a bioinformatics toolkit for processing high-throughput lymphocyte receptor sequencing data.
https://presto.readthedocs.io
GNU Affero General Public License v3.0
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vsearch runUblast incompatibility #50

Closed ssnn-airr closed 7 years ago

ssnn-airr commented 7 years ago

Original report by Anonymous.

presto.Applications.runUBlast -vsearch v2.4.2 no longer supports usearch_local (but there is usearch_global) -see https://github.com/torognes/vsearch/issues/206 for this vsearch bug which means that giving vsearch sequences with '-' will result in stder

ssnn-airr commented 7 years ago

Original comment by Jason Vander Heiden (Bitbucket: javh, GitHub: javh).

@ruoyijiangyale is that you making issues without logging in? :P

IIRC, vsearch has never supported usearch_local. I don't think we can work around that. The solution I went with was to implement blastn support for those tools that needed local alignment.

ssnn-airr commented 7 years ago

Original comment by Jason Vander Heiden (Bitbucket: javh, GitHub: javh).

vsearch doesn't include local alignment support, you need to use blastn instead.