PT  - JOURNAL ARTICLE
AU  - Jacob Pritt
AU  - Ben Langmead
TI  - Boiler: Lossy compression of RNA-seq alignments using coverage vectors
AID  - 10.1101/040634
DP  - 2016 Jan 01
TA  - bioRxiv
PG  - 040634
4099  - http://biorxiv.org/content/early/2016/05/27/040634.short
4100  - http://biorxiv.org/content/early/2016/05/27/040634.full
AB  - We describe Boiler, a new software tool for compressing and querying large collections of RNA-seq alignments. Boiler discards most per-read data, keeping only a genomic coverage vector plus a few empirical distributions summarizing the alignments. Since most per-read data is discarded, storage footprint is often much smaller than that achieved by other compression tools. Despite this, the most relevant per-read data can be recovered; we show that Boiler compression has only a slight negative impact on results given by downstream tools for isoform assembly and quantification. Boiler also allows the user to pose fast and useful queries without decompressing the entire file. Boiler is free open source software available from github.com/jpritt/boiler.