Literature DB >> 25357237

DeeZ: reference-based compression by local assembly.

Faraz Hach1, Ibrahim Numanagić2, S Cenk Sahinalp3.   

Abstract

Mesh：

Year:  2014        PMID： 25357237     DOI： 10.1038/nmeth.3133

Source DB:  PubMed          Journal:  Nat Methods        ISSN： 1548-7091            Impact factor:   28.547


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  8 in total

1.  Large-scale compression of genomic sequence databases with the Burrows-Wheeler transform.

Authors:  Anthony J Cox; Markus J Bauer; Tobias Jakobi; Giovanna Rosone
Journal:  Bioinformatics       Date:  2012-05-03       Impact factor: 6.937

2.  Compressing genomic sequence fragments using SlimGene.

Authors:  Christos Kozanitis; Chris Saunders; Semyon Kruglyak; Vineet Bafna; George Varghese
Journal:  J Comput Biol       Date:  2011-03       Impact factor: 1.479

3.  SCALCE: boosting sequence compression algorithms using locally consistent encoding.

Authors:  Faraz Hach; Ibrahim Numanagic; Can Alkan; S Cenk Sahinalp
Journal:  Bioinformatics       Date:  2012-10-09       Impact factor: 6.937

4.  Compression of DNA sequence reads in FASTQ format.

Authors:  Sebastian Deorowicz; Szymon Grabowski
Journal:  Bioinformatics       Date:  2011-01-19       Impact factor: 6.937

5.  The Sequence Alignment/Map format and SAMtools.

Authors:  Heng Li; Bob Handsaker; Alec Wysoker; Tim Fennell; Jue Ruan; Nils Homer; Gabor Marth; Goncalo Abecasis; Richard Durbin
Journal:  Bioinformatics       Date:  2009-06-08       Impact factor: 6.937

6.  Compression of FASTQ and SAM format sequencing data.

Authors:  James K Bonfield; Matthew V Mahoney
Journal:  PLoS One       Date:  2013-03-22       Impact factor: 3.240

7.  Compression of next-generation sequencing reads aided by highly efficient de novo assembly.

Authors:  Daniel C Jones; Walter L Ruzzo; Xinxia Peng; Michael G Katze
Journal:  Nucleic Acids Res       Date:  2012-08-16       Impact factor: 16.971

8.  The Scramble conversion tool.

Authors:  James K Bonfield
Journal:  Bioinformatics       Date:  2014-06-14       Impact factor: 6.937
  8 in total
  11 in total

1.  Comparison of high-throughput sequencing data compression tools.

Authors:  Ibrahim Numanagić; James K Bonfield; Faraz Hach; Jan Voges; Jörn Ostermann; Claudio Alberti; Marco Mattavelli; S Cenk Sahinalp
Journal:  Nat Methods       Date:  2016-10-24       Impact factor: 28.547

2.  An Evaluation Framework for Lossy Compression of Genome Sequencing Quality Values.

Authors:  Claudio Alberti; Noah Daniels; Mikel Hernaez; Jan Voges; Rachel L Goldfeder; Ana A Hernandez-Lopez; Marco Mattavelli; Bonnie Berger
Journal:  Proc Data Compress Conf       Date:  2016-12-19

3.  CALQ: compression of quality values of aligned sequencing data.

Authors:  Jan Voges; Jörn Ostermann; Mikel Hernaez
Journal:  Bioinformatics       Date:  2018-05-15       Impact factor: 6.937

4.  GeneComp, a new reference-based compressor for SAM files.

Authors:  Reggy Long; Mikel Hernaez; Idoia Ochoa; Tsachy Weissman
Journal:  Proc Data Compress Conf       Date:  2017-05-11

5.  GDC 2: Compression of large collections of genomes.

Authors:  Sebastian Deorowicz; Agnieszka Danek; Marcin Niemiec
Journal:  Sci Rep       Date:  2015-06-25       Impact factor: 4.379

6.  LW-FQZip 2: a parallelized reference-based compression of FASTQ files.

Authors:  Zhi-An Huang; Zhenkun Wen; Qingjin Deng; Ying Chu; Yiwen Sun; Zexuan Zhu
Journal:  BMC Bioinformatics       Date:  2017-03-20       Impact factor: 3.169

7.  CRAM 3.1: Advances in the CRAM File Format.

Authors:  James K Bonfield
Journal:  Bioinformatics       Date:  2022-01-06       Impact factor: 6.937

Review 8.  Novel bioinformatic developments for exome sequencing.

Authors:  Stefan H Lelieveld; Joris A Veltman; Christian Gilissen
Journal:  Hum Genet       Date:  2016-04-13       Impact factor: 4.132

9.  CARGO: effective format-free compressed storage of genomic information.

Authors:  Łukasz Roguski; Paolo Ribeca
Journal:  Nucleic Acids Res       Date:  2016-04-29       Impact factor: 16.971

10.  GABAC: an arithmetic coding solution for genomic data.

Authors:  Jan Voges; Tom Paridaens; Fabian Müntefering; Liudmila S Mainzer; Brian Bliss; Mingyu Yang; Idoia Ochoa; Jan Fostier; Jörn Ostermann; Mikel Hernaez
Journal:  Bioinformatics       Date:  2020-04-01       Impact factor: 6.937
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