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.
Should be able to ungap the reference sequences, build the usearch or blastn database, and then pass the database into the alignment tool, instead of requiring users to maintain a set of both a gapped and ungapped references.
Original comment by Jason Vander Heiden (Bitbucket: javh, GitHub: javh).
Modifications to rebuild database are done. Just need to ungap sequence upon load, test what usearch and makeblastdb do with gapped references, and pass the build through an ungapped temp file, if required.
ssnn-airr
commented
7 years ago
Original report by Jason Vander Heiden (Bitbucket: javh, GitHub: javh).
Should be able to ungap the reference sequences, build the usearch or blastn database, and then pass the database into the alignment tool, instead of requiring users to maintain a set of both a gapped and ungapped references.