Compression of FASTQ and SAM Format Sequencing Data

Storage and transmission of the data produced by modern DNA sequencing instruments has become a major concern, which prompted the Pistoia Alliance to pose the SequenceSqueeze contest for compression of FASTQ files. We present several compression entries from the competition, Fastqz and Samcomp/Fqzco...

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Detalles Bibliográficos
Autores principales: Bonfield, James K., Mahoney, Matthew V.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2013
Materias:
Research Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3606433/
https://www.ncbi.nlm.nih.gov/pubmed/23533605
http://dx.doi.org/10.1371/journal.pone.0059190
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author Bonfield, James K.
Mahoney, Matthew V.
author_facet Bonfield, James K.
Mahoney, Matthew V.
author_sort Bonfield, James K.
collection PubMed
description Storage and transmission of the data produced by modern DNA sequencing instruments has become a major concern, which prompted the Pistoia Alliance to pose the SequenceSqueeze contest for compression of FASTQ files. We present several compression entries from the competition, Fastqz and Samcomp/Fqzcomp, including the winning entry. These are compared against existing algorithms for both reference based compression (CRAM, Goby) and non-reference based compression (DSRC, BAM) and other recently published competition entries (Quip, SCALCE). The tools are shown to be the new Pareto frontier for FASTQ compression, offering state of the art ratios at affordable CPU costs. All programs are freely available on SourceForge. Fastqz: https://sourceforge.net/projects/fastqz/, fqzcomp: https://sourceforge.net/projects/fqzcomp/, and samcomp: https://sourceforge.net/projects/samcomp/.
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spelling pubmed-36064332013-03-26 Compression of FASTQ and SAM Format Sequencing Data Bonfield, James K. Mahoney, Matthew V. PLoS One Research Article Storage and transmission of the data produced by modern DNA sequencing instruments has become a major concern, which prompted the Pistoia Alliance to pose the SequenceSqueeze contest for compression of FASTQ files. We present several compression entries from the competition, Fastqz and Samcomp/Fqzcomp, including the winning entry. These are compared against existing algorithms for both reference based compression (CRAM, Goby) and non-reference based compression (DSRC, BAM) and other recently published competition entries (Quip, SCALCE). The tools are shown to be the new Pareto frontier for FASTQ compression, offering state of the art ratios at affordable CPU costs. All programs are freely available on SourceForge. Fastqz: https://sourceforge.net/projects/fastqz/, fqzcomp: https://sourceforge.net/projects/fqzcomp/, and samcomp: https://sourceforge.net/projects/samcomp/. Public Library of Science 2013-03-22 /pmc/articles/PMC3606433/ /pubmed/23533605 http://dx.doi.org/10.1371/journal.pone.0059190 Text en © 2013 Bonfield, Mahoney http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Bonfield, James K.
Mahoney, Matthew V.
Compression of FASTQ and SAM Format Sequencing Data
title Compression of FASTQ and SAM Format Sequencing Data
title_full Compression of FASTQ and SAM Format Sequencing Data
title_fullStr Compression of FASTQ and SAM Format Sequencing Data
title_full_unstemmed Compression of FASTQ and SAM Format Sequencing Data
title_short Compression of FASTQ and SAM Format Sequencing Data
title_sort compression of fastq and sam format sequencing data
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3606433/
https://www.ncbi.nlm.nih.gov/pubmed/23533605
http://dx.doi.org/10.1371/journal.pone.0059190
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