Boiler: lossy compression of RNA-seq alignments using coverage vectors.
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.
Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21205, USA jacobpritt@gmail.com.
Jacob
J
Pritt
Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21205, USA langmea@cs.jhu.edu.
Ben
B
Langmead
D000465:Algorithms; D000818:Animals; D044962:Data Compression; D004331:Drosophila melanogaster / Q000235:genetics; D049750:Genome, Insect; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D012015:Reference Standards; D016415:Sequence Alignment / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software; D013997:Time Factors
D012333:RNA, Messenger