RT Journal Article
SR Electronic
T1 Boiler: Lossy compression of RNA-seq alignments using coverage vectors
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 040634
DO 10.1101/040634
A1 Jacob Pritt
A1 Ben Langmead
YR 2016
UL http://biorxiv.org/content/early/2016/02/22/040634.abstract
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 quantitation. Boiler also allows the user to pose fast and useful related queries without decompressing the entire file. Boiler is free open source software available from github.com/jpritt/boiler.