Boiler: lossy compression of RNA-seq alignments using coverage vectors.

Jacob Pritt, Ben Langmead

Abstract read

In one paragraph

Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it

0cells of the map it votes in

2citing papers in PubMed

–field-weighted citation impact

1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed.

Gravlax: an annotation-independent molecular evidence archive for single-cell RNA-seq.bioRxiv : the preprint server for biology · 2026
Article
Optimal compressed representation of high throughput sequence data via light assembly.Nature communications · 2018
Article

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

2 authors.

Jacob PrittDepartment of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21205, USA jacobpritt@gmail.com.

Ben LangmeadDepartment 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.

Funding

Hardening and Scaling Core Genomics SoftwareR01GM118568 · NIGMS · JOHNS HOPKINS UNIVERSITY · PI LANGMEAD, BENJAMIN THOMAS · 2016 to 2020

$2.0M

NIGMS NIH HHS R01 GM118568

6 · The paper itself

Abstract

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.

Indexed as

SoftwareAlgorithmsAnimalsData CompressionDrosophila melanogasterGenome, InsectReference StandardsRNA, MessengerSequence AlignmentSequence Analysis, RNATime FactorsRNA, Messenger

Identifiers

PMID27298258

DOI10.1093/nar/gkw540

PMCPMC5027496

What OpenQuestion holds

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LicenceCC BY

Read underepoch 390

Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.