Literature DB >> 35347321

CoLoRd: compressing long reads.

Marek Kokot1, Adam Gudyś1, Heng Li2,3, Sebastian Deorowicz4.   

Abstract

The cost of maintaining exabytes of data produced by sequencing experiments every year has become a major issue in today's genomic research. In spite of the increasing popularity of third-generation sequencing, the existing algorithms for compressing long reads exhibit a minor advantage over the general-purpose gzip. We present CoLoRd, an algorithm able to reduce the size of third-generation sequencing data by an order of magnitude without affecting the accuracy of downstream analyses.
© 2022. The Author(s), under exclusive licence to Springer Nature America, Inc.

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Year:  2022        PMID: 35347321      PMCID: PMC9337911          DOI: 10.1038/s41592-022-01432-3

Source DB:  PubMed          Journal:  Nat Methods        ISSN: 1548-7091            Impact factor:   47.990


  31 in total

1.  The fragment assembly string graph.

Authors:  Eugene W Myers
Journal:  Bioinformatics       Date:  2005-09-01       Impact factor: 6.937

2.  DSRC 2--Industry-oriented compression of FASTQ files.

Authors:  Lukasz Roguski; Sebastian Deorowicz
Journal:  Bioinformatics       Date:  2014-04-18       Impact factor: 6.937

3.  KMC 3: counting and manipulating k-mer statistics.

Authors:  Marek Kokot; Maciej Dlugosz; Sebastian Deorowicz
Journal:  Bioinformatics       Date:  2017-09-01       Impact factor: 6.937

4.  Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm.

Authors:  Haoyu Cheng; Gregory T Concepcion; Xiaowen Feng; Haowen Zhang; Heng Li
Journal:  Nat Methods       Date:  2021-02-01       Impact factor: 28.547

5.  Long-read, whole-genome shotgun sequence data for five model organisms.

Authors:  Kristi E Kim; Paul Peluso; Primo Babayan; P Jane Yeadon; Charles Yu; William W Fisher; Chen-Shan Chin; Nicole A Rapicavoli; David R Rank; Joachim Li; David E A Catcheside; Susan E Celniker; Adam M Phillippy; Casey M Bergman; Jane M Landolin
Journal:  Sci Data       Date:  2014-11-25       Impact factor: 6.444

6.  Nanopore sequencing and assembly of a human genome with ultra-long reads.

Authors:  Miten Jain; Sergey Koren; Karen H Miga; Josh Quick; Arthur C Rand; Thomas A Sasani; John R Tyson; Andrew D Beggs; Alexander T Dilthey; Ian T Fiddes; Sunir Malla; Hannah Marriott; Tom Nieto; Justin O'Grady; Hugh E Olsen; Brent S Pedersen; Arang Rhie; Hollian Richardson; Aaron R Quinlan; Terrance P Snutch; Louise Tee; Benedict Paten; Adam M Phillippy; Jared T Simpson; Nicholas J Loman; Matthew Loose
Journal:  Nat Biotechnol       Date:  2018-01-29       Impact factor: 54.908

7.  An open resource for accurately benchmarking small variant and reference calls.

Authors:  Justin M Zook; Jennifer McDaniel; Nathan D Olson; Justin Wagner; Hemang Parikh; Haynes Heaton; Sean A Irvine; Len Trigg; Rebecca Truty; Cory Y McLean; Francisco M De La Vega; Chunlin Xiao; Stephen Sherry; Marc Salit
Journal:  Nat Biotechnol       Date:  2019-04-01       Impact factor: 54.908

8.  FQSqueezer: k-mer-based compression of sequencing data.

Authors:  Sebastian Deorowicz
Journal:  Sci Rep       Date:  2020-01-17       Impact factor: 4.379

9.  A chromosome-scale assembly of the sorghum genome using nanopore sequencing and optical mapping.

Authors:  Stéphane Deschamps; Yun Zhang; Victor Llaca; Liang Ye; Abhijit Sanyal; Matthew King; Gregory May; Haining Lin
Journal:  Nat Commun       Date:  2018-11-19       Impact factor: 14.919

10.  High quality genome assemblies of Mycoplasma bovis using a taxon-specific Bonito basecaller for MinION and Flongle long-read nanopore sequencing.

Authors:  Nick Vereecke; Jade Bokma; Freddy Haesebrouck; Hans Nauwynck; Filip Boyen; Bart Pardon; Sebastiaan Theuns
Journal:  BMC Bioinformatics       Date:  2020-11-11       Impact factor: 3.169

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