Rxivist combines preprints from bioRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 64,969 bioRxiv papers from 287,914 authors.
Motivation: The past decade has seen an exponential increase in biological sequencing capacity, and there has been a simultaneous effort to help organize and archive some of the vast quantities of sequencing data that are being generated. While these developments are tremendous from the perspective of maximizing the scientific utility of available data, they come with heavy costs. The storage and transmission of such vast amounts of sequencing data is expensive. Results: We present Quark, a semi reference-based compression tool designed for RNA-seq data. Quark makes use of a reference sequence when encoding reads, but produces a representation that can be decoded independently, without the need for a reference. This allows Quark to achieve markedly better compression rates than existing reference-free schemes, while still relieving the burden of assuming a specific, shared reference sequence between the encoder and decoder. We demonstrate that Quark achieves state-of-the-art compression rates, and that, typically, only a small fraction of the reference sequence must be encoded along with the reads to allow reference-free decompression. Availability: Quark is implemented in C++11, and is available under a GPLv3 license at www.github.com/COMBINE-lab/quark.
- Downloaded 574 times
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- Site-wide: 16,793 out of 64,969
- In bioinformatics: 2,575 out of 6,432
- Year to date:
- Site-wide: 59,816 out of 64,969
- Since beginning of last month:
- Site-wide: 54,494 out of 64,969
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- 21 May 2019: PLOS Biology has published a community page about Rxivist.org and its design.
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