Better quality score compression through sequence-based quality smoothing
Identifieur interne : 000387 ( Pmc/Checkpoint ); précédent : 000386; suivant : 000388Better quality score compression through sequence-based quality smoothing
Auteurs : Yoshihiro Shibuya [Italie, France] ; Matteo Comin [Italie]Source :
- BMC Bioinformatics [ 1471-2105 ] ; 2019.
Abstract
Current NGS techniques are becoming exponentially cheaper. As a result, there is an exponential growth of genomic data unfortunately not followed by an exponential growth of storage, leading to the necessity of compression. Most of the entropy of NGS data lies in the quality values associated to each read. Those values are often more diversified than necessary. Because of that, many tools such as Quartz or GeneCodeq, try to change (smooth) quality scores in order to improve compressibility without altering the important information they carry for downstream analysis like SNP calling.
We use the FM-Index, a type of compressed suffix array, to reduce the storage requirements of a dictionary of k-mers and an effective smoothing algorithm to maintain high precision for SNP calling pipelines, while reducing quality scores entropy.
We present YALFF (Yet Another Lossy Fastq Filter), a tool for quality scores compression by smoothing leading to improved compressibility of FASTQ files. The succinct k-mers dictionary allows YALFF to run on consumer computers with only 5.7 GB of available free RAM. YALFF smoothing algorithm can improve genotyping accuracy while using less resources.
The online version of this article (10.1186/s12859-019-2883-5) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s12859-019-2883-5
PubMed: 31757199
PubMed Central: 6873394
Affiliations:
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PMC:6873394Le document en format XML
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Better quality score compression through sequence-based quality smoothing</title>
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<front><div type="abstract" xml:lang="en"><sec><title>Motivation</title>
<p>Current NGS techniques are becoming exponentially cheaper. As a result, there is an exponential growth of genomic data unfortunately not followed by an exponential growth of storage, leading to the necessity of compression. Most of the entropy of NGS data lies in the quality values associated to each read. Those values are often more diversified than necessary. Because of that, many tools such as Quartz or GeneCodeq, try to change (smooth) quality scores in order to improve compressibility without altering the important information they carry for downstream analysis like SNP calling.</p>
</sec>
<sec><title>Results</title>
<p>We use the FM-Index, a type of compressed suffix array, to reduce the storage requirements of a dictionary of k-mers and an effective smoothing algorithm to maintain high precision for SNP calling pipelines, while reducing quality scores entropy.</p>
<p>We present YALFF (Yet Another Lossy Fastq Filter), a tool for quality scores compression by smoothing leading to improved compressibility of FASTQ files. The succinct k-mers dictionary allows YALFF to run on consumer computers with only 5.7 GB of available free RAM. YALFF smoothing algorithm can improve genotyping accuracy while using less resources.</p>
</sec>
<sec><title>Availability</title>
<p><ext-link ext-link-type="uri" xlink:href="https://github.com/yhhshb/yalff">https://github.com/yhhshb/yalff</ext-link>
</p>
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<sec><title>Electronic supplementary material</title>
<p>The online version of this article (10.1186/s12859-019-2883-5) contains supplementary material, which is available to authorized users.</p>
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<back><div1 type="bibliography"><listBibl><biblStruct></biblStruct>
<biblStruct><analytic><author><name sortKey="Ewing, B" uniqKey="Ewing B">B Ewing</name>
</author>
<author><name sortKey="Hillier, L" uniqKey="Hillier L">L Hillier</name>
</author>
<author><name sortKey="Wendl, Mc" uniqKey="Wendl M">MC Wendl</name>
</author>
<author><name sortKey="Green, P" uniqKey="Green P">P Green</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Comin, M" uniqKey="Comin M">M Comin</name>
</author>
<author><name sortKey="Leoni, A" uniqKey="Leoni A">A Leoni</name>
</author>
<author><name sortKey="Schimd, M" uniqKey="Schimd M">M Schimd</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Comin, M" uniqKey="Comin M">M Comin</name>
</author>
<author><name sortKey="Leoni, A" uniqKey="Leoni A">A Leoni</name>
</author>
<author><name sortKey="Schimd, M" uniqKey="Schimd M">M Schimd</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Schimd, M" uniqKey="Schimd M">M Schimd</name>
</author>
<author><name sortKey="Comin, M" uniqKey="Comin M">M Comin</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Malysa, G" uniqKey="Malysa G">G Malysa</name>
</author>
<author><name sortKey="Hernaez, M" uniqKey="Hernaez M">M Hernaez</name>
</author>
<author><name sortKey="Ochoa, I" uniqKey="Ochoa I">I Ochoa</name>
</author>
<author><name sortKey="Rao, M" uniqKey="Rao M">M Rao</name>
</author>
<author><name sortKey="Ganesan, K" uniqKey="Ganesan K">K Ganesan</name>
</author>
<author><name sortKey="Weissman, T" uniqKey="Weissman T">T Weissman</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Roguski, L" uniqKey="Roguski L">L Roguski</name>
</author>
<author><name sortKey="Ochoa, I" uniqKey="Ochoa I">I Ochoa</name>
</author>
<author><name sortKey="Hernaez, M" uniqKey="Hernaez M">M Hernaez</name>
</author>
<author><name sortKey="Deorowicz, S" uniqKey="Deorowicz S">S Deorowicz</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Holley, G" uniqKey="Holley G">G Holley</name>
</author>
<author><name sortKey="Wittler, R" uniqKey="Wittler R">R Wittler</name>
</author>
<author><name sortKey="Stoye, J" uniqKey="Stoye J">J Stoye</name>
</author>
<author><name sortKey="Hach, F" uniqKey="Hach F">F Hach</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Grabowski, S" uniqKey="Grabowski S">S Grabowski</name>
</author>
<author><name sortKey="Deorowicz, S" uniqKey="Deorowicz S">S Deorowicz</name>
</author>
<author><name sortKey="Roguski, L" uniqKey="Roguski L">L Roguski</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Hach, F" uniqKey="Hach F">F Hach</name>
</author>
<author><name sortKey="Numanagi, I" uniqKey="Numanagi I">I Numanagić</name>
</author>
<author><name sortKey="Alkan, C" uniqKey="Alkan C">C Alkan</name>
</author>
<author><name sortKey="Sahinalp, Sc" uniqKey="Sahinalp S">SC Sahinalp</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Greenfield, Dl" uniqKey="Greenfield D">DL Greenfield</name>
</author>
<author><name sortKey="Stegle, O" uniqKey="Stegle O">O Stegle</name>
</author>
<author><name sortKey="Rrustemi, A" uniqKey="Rrustemi A">A Rrustemi</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Yu, Yw" uniqKey="Yu Y">YW Yu</name>
</author>
<author><name sortKey="Yorukoglu, D" uniqKey="Yorukoglu D">D Yorukoglu</name>
</author>
<author><name sortKey="Peng, J" uniqKey="Peng J">J Peng</name>
</author>
<author><name sortKey="Berger, B" uniqKey="Berger B">B Berger</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Bonfield, James K" uniqKey="Bonfield J">James K. Bonfield</name>
</author>
<author><name sortKey="Mahoney, Matthew V" uniqKey="Mahoney M">Matthew V. Mahoney</name>
</author>
</analytic>
</biblStruct>
<biblStruct></biblStruct>
<biblStruct><analytic><author><name sortKey="Canovas, R" uniqKey="Canovas R">R Cánovas</name>
</author>
<author><name sortKey="Moffat, A" uniqKey="Moffat A">A Moffat</name>
</author>
<author><name sortKey="Turpin, A" uniqKey="Turpin A">A Turpin</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Ochoa, I" uniqKey="Ochoa I">I Ochoa</name>
</author>
<author><name sortKey="Asnani, H" uniqKey="Asnani H">H Asnani</name>
</author>
<author><name sortKey="Bharadia, D" uniqKey="Bharadia D">D Bharadia</name>
</author>
<author><name sortKey="Chowdhury, M" uniqKey="Chowdhury M">M Chowdhury</name>
</author>
<author><name sortKey="Weissman, T" uniqKey="Weissman T">T Weissman</name>
</author>
<author><name sortKey="Yona, G" uniqKey="Yona G">G Yona</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Ochoa, I" uniqKey="Ochoa I">I Ochoa</name>
</author>
<author><name sortKey="Hernaez, M" uniqKey="Hernaez M">M Hernaez</name>
</author>
<author><name sortKey="Goldfeder, R" uniqKey="Goldfeder R">R Goldfeder</name>
</author>
<author><name sortKey="Weissman, T" uniqKey="Weissman T">T Weissman</name>
</author>
<author><name sortKey="Ashley, E" uniqKey="Ashley E">E Ashley</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Janin, L" uniqKey="Janin L">L Janin</name>
</author>
<author><name sortKey="Rosone, G" uniqKey="Rosone G">G Rosone</name>
</author>
<author><name sortKey="Cox, Aj" uniqKey="Cox A">AJ Cox</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Benoit, G" uniqKey="Benoit G">G Benoit</name>
</author>
<author><name sortKey="Lemaitre, C" uniqKey="Lemaitre C">C Lemaitre</name>
</author>
<author><name sortKey="Lavenier, D" uniqKey="Lavenier D">D Lavenier</name>
</author>
<author><name sortKey="Drezen, E" uniqKey="Drezen E">E Drezen</name>
</author>
<author><name sortKey="Dayris, T" uniqKey="Dayris T">T Dayris</name>
</author>
<author><name sortKey="Uricaru, R" uniqKey="Uricaru R">R Uricaru</name>
</author>
<author><name sortKey="Rizk, G" uniqKey="Rizk G">G Rizk</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Yu, Yw" uniqKey="Yu Y">YW Yu</name>
</author>
<author><name sortKey="Yorukoglu, D" uniqKey="Yorukoglu D">D Yorukoglu</name>
</author>
<author><name sortKey="Berger, B" uniqKey="Berger B">B Berger</name>
</author>
</analytic>
</biblStruct>
<biblStruct></biblStruct>
<biblStruct><analytic><author><name sortKey="Comin, M" uniqKey="Comin M">M Comin</name>
</author>
<author><name sortKey="Schimd, M" uniqKey="Schimd M">M Schimd</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Comin, M" uniqKey="Comin M">M Comin</name>
</author>
<author><name sortKey="Verzotto, D" uniqKey="Verzotto D">D Verzotto</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Girotto, S" uniqKey="Girotto S">S Girotto</name>
</author>
<author><name sortKey="Comin, M" uniqKey="Comin M">M Comin</name>
</author>
<author><name sortKey="Pizzi, C" uniqKey="Pizzi C">C Pizzi</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Qian, J" uniqKey="Qian J">J Qian</name>
</author>
<author><name sortKey="Marchiori, D" uniqKey="Marchiori D">D Marchiori</name>
</author>
<author><name sortKey="Comin, M" uniqKey="Comin M">M Comin</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Shibuya, Y" uniqKey="Shibuya Y">Y Shibuya</name>
</author>
<author><name sortKey="Comin, M" uniqKey="Comin M">M Comin</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Li, H" uniqKey="Li H">H Li</name>
</author>
<author><name sortKey="Durbin, R" uniqKey="Durbin R">R Durbin</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Li, H" uniqKey="Li H">H Li</name>
</author>
<author><name sortKey="Durbin, R" uniqKey="Durbin R">R Durbin</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Marcais, G" uniqKey="Marcais G">G Marçais</name>
</author>
<author><name sortKey="Kingsford, C" uniqKey="Kingsford C">C Kingsford</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Ferragina, P" uniqKey="Ferragina P">P Ferragina</name>
</author>
<author><name sortKey="Manzini, G" uniqKey="Manzini G">G Manzini</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Ferragina, P" uniqKey="Ferragina P">P Ferragina</name>
</author>
<author><name sortKey="Manzini, G" uniqKey="Manzini G">G Manzini</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Li, H" uniqKey="Li H">H Li</name>
</author>
<author><name sortKey="Durbin, R" uniqKey="Durbin R">R Durbin</name>
</author>
</analytic>
</biblStruct>
</listBibl>
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<front><journal-meta><journal-id journal-id-type="nlm-ta">BMC Bioinformatics</journal-id>
<journal-id journal-id-type="iso-abbrev">BMC Bioinformatics</journal-id>
<journal-title-group><journal-title>BMC Bioinformatics</journal-title>
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<issn pub-type="epub">1471-2105</issn>
<publisher><publisher-name>BioMed Central</publisher-name>
<publisher-loc>London</publisher-loc>
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<article-id pub-id-type="pmc">6873394</article-id>
<article-id pub-id-type="publisher-id">2883</article-id>
<article-id pub-id-type="doi">10.1186/s12859-019-2883-5</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Research</subject>
</subj-group>
</article-categories>
<title-group><article-title>Better quality score compression through sequence-based quality smoothing</article-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Shibuya</surname>
<given-names>Yoshihiro</given-names>
</name>
<address><email>yoshihiro.shibuya@studenti.unipd.it</email>
</address>
<xref ref-type="aff" rid="Aff1">1</xref>
<xref ref-type="aff" rid="Aff2">2</xref>
</contrib>
<contrib contrib-type="author" corresp="yes"><name><surname>Comin</surname>
<given-names>Matteo</given-names>
</name>
<address><email>comin@dei.unipd.it</email>
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<xref ref-type="aff" rid="Aff1">1</xref>
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<aff id="Aff1"><label>1</label>
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<institution>Department of Information Engineering, University of Padova,</institution>
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via Gradenigo 6/A, Padova, Italy</aff>
<aff id="Aff2"><label>2</label>
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Bâtiment Copernic - 5, bd Descartes, Champs sur Marne, France</aff>
</contrib-group>
<pub-date pub-type="epub"><day>22</day>
<month>11</month>
<year>2019</year>
</pub-date>
<pub-date pub-type="pmc-release"><day>22</day>
<month>11</month>
<year>2019</year>
</pub-date>
<pub-date pub-type="collection"><year>2019</year>
</pub-date>
<volume>20</volume>
<issue>Suppl 9</issue>
<issue-sponsor>Publication of this supplement has not been supported by sponsorship. Information about the source of funding for publication charges can be found in the individual articles. The articles have undergone the journal's standard peer review process for supplements. The Supplement Editors declare that they have no competing interests.</issue-sponsor>
<elocation-id>302</elocation-id>
<history><date date-type="received"><day>30</day>
<month>4</month>
<year>2019</year>
</date>
<date date-type="accepted"><day>7</day>
<month>5</month>
<year>2019</year>
</date>
</history>
<permissions><copyright-statement>© The Author(s) 2019</copyright-statement>
<license license-type="OpenAccess"><license-p><bold>Open Access</bold>
This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">http://creativecommons.org/licenses/by/4.0/</ext-link>
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<abstract id="Abs1"><sec><title>Motivation</title>
<p>Current NGS techniques are becoming exponentially cheaper. As a result, there is an exponential growth of genomic data unfortunately not followed by an exponential growth of storage, leading to the necessity of compression. Most of the entropy of NGS data lies in the quality values associated to each read. Those values are often more diversified than necessary. Because of that, many tools such as Quartz or GeneCodeq, try to change (smooth) quality scores in order to improve compressibility without altering the important information they carry for downstream analysis like SNP calling.</p>
</sec>
<sec><title>Results</title>
<p>We use the FM-Index, a type of compressed suffix array, to reduce the storage requirements of a dictionary of k-mers and an effective smoothing algorithm to maintain high precision for SNP calling pipelines, while reducing quality scores entropy.</p>
<p>We present YALFF (Yet Another Lossy Fastq Filter), a tool for quality scores compression by smoothing leading to improved compressibility of FASTQ files. The succinct k-mers dictionary allows YALFF to run on consumer computers with only 5.7 GB of available free RAM. YALFF smoothing algorithm can improve genotyping accuracy while using less resources.</p>
</sec>
<sec><title>Availability</title>
<p><ext-link ext-link-type="uri" xlink:href="https://github.com/yhhshb/yalff">https://github.com/yhhshb/yalff</ext-link>
</p>
</sec>
<sec><title>Electronic supplementary material</title>
<p>The online version of this article (10.1186/s12859-019-2883-5) contains supplementary material, which is available to authorized users.</p>
</sec>
</abstract>
<kwd-group xml:lang="en"><title>Keywords</title>
<kwd>FASTQ compression</kwd>
<kwd>BWT</kwd>
<kwd>FM-Index</kwd>
</kwd-group>
<conference xlink:href="http://bioinformatics.it/"><conf-name>Annual Meeting of the Bioinformatics Italian Society (BITS 2018)</conf-name>
<conf-acronym>BITS 2018</conf-acronym>
<conf-loc>Turin, Italy</conf-loc>
<conf-date>27 - 29 June 2018</conf-date>
</conference>
<custom-meta-group><custom-meta><meta-name>issue-copyright-statement</meta-name>
<meta-value>© The Author(s) 2019</meta-value>
</custom-meta>
</custom-meta-group>
</article-meta>
</front>
</pmc>
<affiliations><list><country><li>France</li>
<li>Italie</li>
</country>
</list>
<tree><country name="Italie"><noRegion><name sortKey="Shibuya, Yoshihiro" sort="Shibuya, Yoshihiro" uniqKey="Shibuya Y" first="Yoshihiro" last="Shibuya">Yoshihiro Shibuya</name>
</noRegion>
<name sortKey="Comin, Matteo" sort="Comin, Matteo" uniqKey="Comin M" first="Matteo" last="Comin">Matteo Comin</name>
</country>
<country name="France"><noRegion><name sortKey="Shibuya, Yoshihiro" sort="Shibuya, Yoshihiro" uniqKey="Shibuya Y" first="Yoshihiro" last="Shibuya">Yoshihiro Shibuya</name>
</noRegion>
</country>
</tree>
</affiliations>
</record>
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