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.
A minlen capability added to maskPrimers-align would
1 - increase speed ?
2 - obviate some post-processing
Use case:
Single cell data uses mixed-length barcodes, to increase the barcode space and add nucleotide diversity (for the sequence). The barcode is called by aligning a long constant sequence that is 3' in the read with maskPrimers-align+cut, then I post-process results with a one-liner to filter for barcodes of a certain length... which works fine but involves non-pRESTO code.
just a suggestion; not high priority at al.
ssnn-airr
commented
6 years ago
Original report by Anonymous.
A minlen capability added to maskPrimers-align would 1 - increase speed ? 2 - obviate some post-processing
Use case: Single cell data uses mixed-length barcodes, to increase the barcode space and add nucleotide diversity (for the sequence). The barcode is called by aligning a long constant sequence that is 3' in the read with maskPrimers-align+cut, then I post-process results with a one-liner to filter for barcodes of a certain length... which works fine but involves non-pRESTO code. just a suggestion; not high priority at al.