6 citations · 26 across the 22 of their papers we have counts for
4 papers · 1 filter
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…
Compressing and Indexing Aligned Readsets
Travis Gagie, Garance Gourdel, Giovanni Manzini
In this paper we show how to use one or more assembled or partially assembled genome as the basis for a compressed full-text index of its readset. Specifically, we build a labelled…
External memory BWT and LCP computation for sequence collections with applications
Lavinia Egidi, Felipe A. Louza, Giovanni Manzini +1
We propose an external memory algorithm for the computation of the BWT and LCP array for a collection of sequences. Our algorithm takes the amount of available memory as an input p…
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…