Evidence map›Paper›PMID 31099383›Full record

ArticleBioinformatics (Oxford, England)2019

Cram-JS: reference-based decompression in node and the browser.

Robert Buels, Shihab Dider, Colin Diesh, James Robinson, Ian Holmes

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Bioinformatics (Oxford, England), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. 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

5 authors.

Robert BuelsDepartment of Bioengineering, University of California, Berkeley, Berkeley, CA, USA.
Shihab DiderDepartment of Bioengineering, University of California, Berkeley, Berkeley, CA, USA.
Colin DieshDepartment of Bioengineering, University of California, Berkeley, Berkeley, CA, USA.
James RobinsonBroad Institute, Cambridge, MA, USA.
Ian HolmesDepartment of Bioengineering, University of California, Berkeley, Berkeley, CA, USA.

Funding

Web-based visualization of coronavirus genomes and proteinsR01HG004483 · NHGRI · UNIVERSITY OF CALIFORNIA BERKELEY · PI Ian H Holmes · 2007 to 2026
$9.3M
Novel Web-based Tools for Collaborative Community-Driven Genome Feature AnnotatioR01GM080203 · NIGMS · UNIVERSITY OF CALIFORNIA BERKELEY · PI Ian H Holmes · 2007 to 2026
$8.5M
Developing the JBrowse Genome Browser to Visualize Structural Variants and Cancer Genomics DataU24CA220441 · NCI · UNIVERSITY OF CALIFORNIA BERKELEY · PI HOLMES, IAN H, STEIN, LINCOLN D. · 2017 to 2020
$2.7M
NCI NIH HHS U24 CA220441NHGRI NIH HHS R01 HG004483NIGMS NIH HHS R01 GM080203Wellcome Trust
6 · The paper itself

Abstract

motivationThe CRAM format addresses rising DNA storage costs for short-read sequencing by aligning reads to a reference genome and encoding the resulting alignment with Huffman, subexponential, Elias gamma, rANS, gzip and other codes. The CRAM codec is complex, and until now, there has been no JavaScript implementation.

resultsWe have developed a JavaScript library, Cram-JS, that natively reads and decompresses the CRAM format on-the-fly. The library is used in the JBrowse and IGV-JS genome browsers and can readily be used by other JavaScript applications, in the web browser or in Node. AVAILABILITY AND IMPLEMENTATION: Cram-JS is written to the ES-6 standard and is available from the GitHub repository at https://github.com/GMOD/cram-js.

Indexed as

GenomeSoftwareDNAWeb BrowserDNA

Identifiers

PMID31099383
PMCPMC6821367

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

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.