Efficient Construction of a Complete Index for Pan-Genomics Read Alignment.

ABSTRACT: Short-read aligners predominantly use the FM-index, which is easily able to index one or a few human genomes. However, it does not scale well to indexing collections of thousands of genomes. Driving this issue are the two chief components of the index: (1) a rank data structure over the Burrows-Wheeler Transform (BWT) of the string that will allow us to find the interval in the string's suffix array (SA), and (2) a sample of the SA that-when used with the rank data structure-allows us to access the SA. The rank data structure can be kept small even for large genomic databases, by run-length compressing the BWT, but until recently there was no means known to keep the SA sample small without greatly slowing down access to the SA. Now that (SODA 2018) has defined an SA sample that takes ab

SUBMITTER: Kuhnle A 

PROVIDER: S-EPMC7185338 | biostudies-literature | 2020 Apr

REPOSITORIES: biostudies-literature