SimkaMin: fast and resource frugal de novo comparative metagenomics.
Identifieur interne : 000080 ( PubMed/Checkpoint ); précédent : 000079; suivant : 000081SimkaMin: fast and resource frugal de novo comparative metagenomics.
Auteurs : Gaëtan Benoit [France] ; Mahendra Mariadassou [France] ; Stéphane Robin [France] ; Sophie Schbath [France] ; Pierre Peterlongo [France] ; Claire Lemaitre [France]Source :
- Bioinformatics (Oxford, England) [ 1367-4811 ] ; 2020.
Abstract
De novo comparative metagenomics is one of the most straightforward ways to analyze large sets of metagenomic data. Latest methods use the fraction of shared k-mers to estimate genomic similarity between read sets. However, those methods, while extremely efficient, are still limited by computational needs for practical usage outside of large computing facilities.
DOI: 10.1093/bioinformatics/btz685
PubMed: 31504187
Affiliations:
Links toward previous steps (curation, corpus...)
Links to Exploration step
pubmed:31504187Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">SimkaMin: fast and resource frugal de novo comparative metagenomics.</title><author><name sortKey="Benoit, Gaetan" sort="Benoit, Gaetan" uniqKey="Benoit G" first="Gaëtan" last="Benoit">Gaëtan Benoit</name><affiliation wicri:level="3"><nlm:affiliation>Univ Rennes, Inria, CNRS, IRISA, F-35000 Rennes, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Univ Rennes, Inria, CNRS, IRISA, F-35000 Rennes</wicri:regionArea><placeName><region type="region" nuts="2">Région Bretagne</region><settlement type="city">Rennes</settlement></placeName></affiliation></author><author><name sortKey="Mariadassou, Mahendra" sort="Mariadassou, Mahendra" uniqKey="Mariadassou M" first="Mahendra" last="Mariadassou">Mahendra Mariadassou</name><affiliation wicri:level="3"><nlm:affiliation>MaIAGE, INRA, Université Paris-Saclay, 78350 Jouy-en-Josas, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>MaIAGE, INRA, Université Paris-Saclay, 78350 Jouy-en-Josas</wicri:regionArea><placeName><region type="region" nuts="2">Île-de-France</region><settlement type="city">Jouy-en-Josas</settlement></placeName></affiliation></author><author><name sortKey="Robin, Stephane" sort="Robin, Stephane" uniqKey="Robin S" first="Stéphane" last="Robin">Stéphane Robin</name><affiliation wicri:level="3"><nlm:affiliation>UMR MIA-Paris, AgroParisTech, INRA, Université Paris-Saclay, 75005 Paris, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>UMR MIA-Paris, AgroParisTech, INRA, Université Paris-Saclay, 75005 Paris</wicri:regionArea><placeName><region type="region" nuts="2">Île-de-France</region><settlement type="city">Paris</settlement></placeName></affiliation></author><author><name sortKey="Schbath, Sophie" sort="Schbath, Sophie" uniqKey="Schbath S" first="Sophie" last="Schbath">Sophie Schbath</name><affiliation wicri:level="3"><nlm:affiliation>MaIAGE, INRA, Université Paris-Saclay, 78350 Jouy-en-Josas, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>MaIAGE, INRA, Université Paris-Saclay, 78350 Jouy-en-Josas</wicri:regionArea><placeName><region type="region" nuts="2">Île-de-France</region><settlement type="city">Jouy-en-Josas</settlement></placeName></affiliation></author><author><name sortKey="Peterlongo, Pierre" sort="Peterlongo, Pierre" uniqKey="Peterlongo P" first="Pierre" last="Peterlongo">Pierre Peterlongo</name><affiliation wicri:level="3"><nlm:affiliation>Univ Rennes, Inria, CNRS, IRISA, F-35000 Rennes, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Univ Rennes, Inria, CNRS, IRISA, F-35000 Rennes</wicri:regionArea><placeName><region type="region" nuts="2">Région Bretagne</region><settlement type="city">Rennes</settlement></placeName></affiliation></author><author><name sortKey="Lemaitre, Claire" sort="Lemaitre, Claire" uniqKey="Lemaitre C" first="Claire" last="Lemaitre">Claire Lemaitre</name><affiliation wicri:level="3"><nlm:affiliation>Univ Rennes, Inria, CNRS, IRISA, F-35000 Rennes, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Univ Rennes, Inria, CNRS, IRISA, F-35000 Rennes</wicri:regionArea><placeName><region type="region" nuts="2">Région Bretagne</region><settlement type="city">Rennes</settlement></placeName></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2020">2020</date><idno type="RBID">pubmed:31504187</idno><idno type="pmid">31504187</idno><idno type="doi">10.1093/bioinformatics/btz685</idno><idno type="wicri:Area/PubMed/Corpus">000423</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000423</idno><idno type="wicri:Area/PubMed/Curation">000423</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">000423</idno><idno type="wicri:Area/PubMed/Checkpoint">000080</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">000080</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">SimkaMin: fast and resource frugal de novo comparative metagenomics.</title><author><name sortKey="Benoit, Gaetan" sort="Benoit, Gaetan" uniqKey="Benoit G" first="Gaëtan" last="Benoit">Gaëtan Benoit</name><affiliation wicri:level="3"><nlm:affiliation>Univ Rennes, Inria, CNRS, IRISA, F-35000 Rennes, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Univ Rennes, Inria, CNRS, IRISA, F-35000 Rennes</wicri:regionArea><placeName><region type="region" nuts="2">Région Bretagne</region><settlement type="city">Rennes</settlement></placeName></affiliation></author><author><name sortKey="Mariadassou, Mahendra" sort="Mariadassou, Mahendra" uniqKey="Mariadassou M" first="Mahendra" last="Mariadassou">Mahendra Mariadassou</name><affiliation wicri:level="3"><nlm:affiliation>MaIAGE, INRA, Université Paris-Saclay, 78350 Jouy-en-Josas, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>MaIAGE, INRA, Université Paris-Saclay, 78350 Jouy-en-Josas</wicri:regionArea><placeName><region type="region" nuts="2">Île-de-France</region><settlement type="city">Jouy-en-Josas</settlement></placeName></affiliation></author><author><name sortKey="Robin, Stephane" sort="Robin, Stephane" uniqKey="Robin S" first="Stéphane" last="Robin">Stéphane Robin</name><affiliation wicri:level="3"><nlm:affiliation>UMR MIA-Paris, AgroParisTech, INRA, Université Paris-Saclay, 75005 Paris, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>UMR MIA-Paris, AgroParisTech, INRA, Université Paris-Saclay, 75005 Paris</wicri:regionArea><placeName><region type="region" nuts="2">Île-de-France</region><settlement type="city">Paris</settlement></placeName></affiliation></author><author><name sortKey="Schbath, Sophie" sort="Schbath, Sophie" uniqKey="Schbath S" first="Sophie" last="Schbath">Sophie Schbath</name><affiliation wicri:level="3"><nlm:affiliation>MaIAGE, INRA, Université Paris-Saclay, 78350 Jouy-en-Josas, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>MaIAGE, INRA, Université Paris-Saclay, 78350 Jouy-en-Josas</wicri:regionArea><placeName><region type="region" nuts="2">Île-de-France</region><settlement type="city">Jouy-en-Josas</settlement></placeName></affiliation></author><author><name sortKey="Peterlongo, Pierre" sort="Peterlongo, Pierre" uniqKey="Peterlongo P" first="Pierre" last="Peterlongo">Pierre Peterlongo</name><affiliation wicri:level="3"><nlm:affiliation>Univ Rennes, Inria, CNRS, IRISA, F-35000 Rennes, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Univ Rennes, Inria, CNRS, IRISA, F-35000 Rennes</wicri:regionArea><placeName><region type="region" nuts="2">Région Bretagne</region><settlement type="city">Rennes</settlement></placeName></affiliation></author><author><name sortKey="Lemaitre, Claire" sort="Lemaitre, Claire" uniqKey="Lemaitre C" first="Claire" last="Lemaitre">Claire Lemaitre</name><affiliation wicri:level="3"><nlm:affiliation>Univ Rennes, Inria, CNRS, IRISA, F-35000 Rennes, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Univ Rennes, Inria, CNRS, IRISA, F-35000 Rennes</wicri:regionArea><placeName><region type="region" nuts="2">Région Bretagne</region><settlement type="city">Rennes</settlement></placeName></affiliation></author></analytic><series><title level="j">Bioinformatics (Oxford, England)</title><idno type="eISSN">1367-4811</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">De novo comparative metagenomics is one of the most straightforward ways to analyze large sets of metagenomic data. Latest methods use the fraction of shared k-mers to estimate genomic similarity between read sets. However, those methods, while extremely efficient, are still limited by computational needs for practical usage outside of large computing facilities.</div></front></TEI><pubmed><MedlineCitation Status="In-Data-Review" Owner="NLM"><PMID Version="1">31504187</PMID><DateRevised><Year>2020</Year><Month>02</Month><Day>20</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Electronic">1367-4811</ISSN><JournalIssue CitedMedium="Internet"><Volume>36</Volume><Issue>4</Issue><PubDate><Year>2020</Year><Month>Feb</Month><Day>15</Day></PubDate></JournalIssue><Title>Bioinformatics (Oxford, England)</Title><ISOAbbreviation>Bioinformatics</ISOAbbreviation></Journal><ArticleTitle>SimkaMin: fast and resource frugal de novo comparative metagenomics.</ArticleTitle><Pagination><MedlinePgn>1275-1276</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1093/bioinformatics/btz685</ELocationID><Abstract><AbstractText Label="MOTIVATION" NlmCategory="BACKGROUND">De novo comparative metagenomics is one of the most straightforward ways to analyze large sets of metagenomic data. Latest methods use the fraction of shared k-mers to estimate genomic similarity between read sets. However, those methods, while extremely efficient, are still limited by computational needs for practical usage outside of large computing facilities.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">We present SimkaMin, a quick comparative metagenomics tool with low disk and memory footprints, thanks to an efficient data subsampling scheme used to estimate Bray-Curtis and Jaccard dissimilarities. One billion metagenomic reads can be analyzed in <3 min, with tiny memory (1.09 GB) and disk (≈0.3 GB) requirements and without altering the quality of the downstream comparative analyses, making of SimkaMin a tool perfectly tailored for very large-scale metagenomic projects.</AbstractText><AbstractText Label="AVAILABILITY AND IMPLEMENTATION" NlmCategory="METHODS">https://github.com/GATB/simka.</AbstractText><AbstractText Label="SUPPLEMENTARY INFORMATION" NlmCategory="BACKGROUND">Supplementary data are available at Bioinformatics online.</AbstractText><CopyrightInformation>© The Author(s) 2019. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Benoit</LastName><ForeName>Gaëtan</ForeName><Initials>G</Initials><AffiliationInfo><Affiliation>Univ Rennes, Inria, CNRS, IRISA, F-35000 Rennes, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Mariadassou</LastName><ForeName>Mahendra</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>MaIAGE, INRA, Université Paris-Saclay, 78350 Jouy-en-Josas, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Robin</LastName><ForeName>Stéphane</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>UMR MIA-Paris, AgroParisTech, INRA, Université Paris-Saclay, 75005 Paris, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Schbath</LastName><ForeName>Sophie</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>MaIAGE, INRA, Université Paris-Saclay, 78350 Jouy-en-Josas, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Peterlongo</LastName><ForeName>Pierre</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>Univ Rennes, Inria, CNRS, IRISA, F-35000 Rennes, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lemaitre</LastName><ForeName>Claire</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Univ Rennes, Inria, CNRS, IRISA, F-35000 Rennes, France.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Bioinformatics</MedlineTA><NlmUniqueID>9808944</NlmUniqueID><ISSNLinking>1367-4803</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2019</Year><Month>06</Month><Day>14</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2019</Year><Month>07</Month><Day>19</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2019</Year><Month>08</Month><Day>29</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2019</Year><Month>9</Month><Day>11</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2019</Year><Month>9</Month><Day>11</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2019</Year><Month>9</Month><Day>11</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">31504187</ArticleId><ArticleId IdType="pii">5559271</ArticleId><ArticleId IdType="doi">10.1093/bioinformatics/btz685</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>France</li></country><region><li>Région Bretagne</li><li>Île-de-France</li></region><settlement><li>Jouy-en-Josas</li><li>Paris</li><li>Rennes</li></settlement></list><tree><country name="France"><region name="Région Bretagne"><name sortKey="Benoit, Gaetan" sort="Benoit, Gaetan" uniqKey="Benoit G" first="Gaëtan" last="Benoit">Gaëtan Benoit</name></region><name sortKey="Lemaitre, Claire" sort="Lemaitre, Claire" uniqKey="Lemaitre C" first="Claire" last="Lemaitre">Claire Lemaitre</name><name sortKey="Mariadassou, Mahendra" sort="Mariadassou, Mahendra" uniqKey="Mariadassou M" first="Mahendra" last="Mariadassou">Mahendra Mariadassou</name><name sortKey="Peterlongo, Pierre" sort="Peterlongo, Pierre" uniqKey="Peterlongo P" first="Pierre" last="Peterlongo">Pierre Peterlongo</name><name sortKey="Robin, Stephane" sort="Robin, Stephane" uniqKey="Robin S" first="Stéphane" last="Robin">Stéphane Robin</name><name sortKey="Schbath, Sophie" sort="Schbath, Sophie" uniqKey="Schbath S" first="Sophie" last="Schbath">Sophie Schbath</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/PubMed/Checkpoint
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000080 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/PubMed/Checkpoint/biblio.hfd -nk 000080 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Sante
|area= MersV1
|flux= PubMed
|étape= Checkpoint
|type= RBID
|clé= pubmed:31504187
|texte= SimkaMin: fast and resource frugal de novo comparative metagenomics.
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/PubMed/Checkpoint/RBID.i -Sk "pubmed:31504187" \
| HfdSelect -Kh $EXPLOR_AREA/Data/PubMed/Checkpoint/biblio.hfd \
| NlmPubMed2Wicri -a MersV1
| This area was generated with Dilib version V0.6.33. |  |