4 papers
PHONI: Streamed Matching Statistics with Multi-Genome References
Christina Boucher, Travis Gagie, Tomohiro I +6
Computing the matching statistics of patterns with respect to a text is a fundamental task in bioinformatics, but a formidable one when the text is a highly compressed genomic data…
Matching reads to many genomes with the -index
Taher Mun, Alan Kuhnle, Christina Boucher +3
The -index is a tool for compressed indexing of genomic databases for exact pattern matching, which can be used to completely align reads that perfectly match some part of a gen…
Efficient Construction of a Complete Index for Pan-Genomics Read Alignment
Alan Kuhnle, Taher Mun, Christina Boucher +3
While short read aligners, which predominantly use the FM-index, are able to easily index one or a few human genomes, they do not scale well to indexing databases containing thousa…
Prefix-Free Parsing for Building Big BWTs
Christina Boucher, Travis Gagie, Alan Kuhnle +3
High-throughput sequencing technologies have led to explosive growth of genomic databases; one of which will soon reach hundreds of terabytes. For many applications we want to buil…