K-mer clustering algorithm using a MapReduce framework: application to the parallelization of the Inchworm module of Trinity
Identifieur interne : 000D26 ( Main/Exploration ); précédent : 000D25; suivant : 000D27K-mer clustering algorithm using a MapReduce framework: application to the parallelization of the Inchworm module of Trinity
Auteurs : Chang Sik Kim [Royaume-Uni] ; Martyn D. Winn ; Vipin Sachdeva [États-Unis] ; Kirk E. Jordan [États-Unis]Source :
- BMC Bioinformatics [ 1471-2105 ] ; 2017.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : RNA.
- chemical , genetics : RNA.
- Algorithms, Cluster Analysis, High-Throughput Nucleotide Sequencing, Sequence Analysis, RNA, Transcriptome.
Abstract
De novo transcriptome assembly is an important technique for understanding gene expression in non-model organisms. Many de novo assemblers using the de Bruijn graph of a set of the RNA sequences rely on in-memory representation of this graph. However, current methods analyse the complete set of read-derived k-mer sequence at once, resulting in the need for computer hardware with large shared memory.
We introduce a novel approach that clusters k-mers as the first step. The clusters correspond to small sets of gene products, which can be processed quickly to give candidate transcripts. We implement the clustering step using the MapReduce approach for parallelising the analysis of large datasets, which enables the use of compute clusters. The computational task is distributed across the compute system using the industry-standard MPI protocol, and no specialised hardware is required. Using this approach, we have re-implemented the Inchworm module from the widely used Trinity pipeline, and tested the method in the context of the full Trinity pipeline. Validation tests on a range of real datasets show large reductions in the runtime and per-node memory requirements, when making use of a compute cluster.
Our study shows that MapReduce-based clustering has great potential for distributing challenging sequencing problems, without loss of accuracy. Although we have focussed on the Trinity package, we propose that such clustering is a useful initial step for other assembly pipelines.
The online version of this article (10.1186/s12859-017-1881-8) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s12859-017-1881-8
PubMed: 29100493
PubMed Central: 5670514
Affiliations:
Links toward previous steps (curation, corpus...)
- to stream Pmc, to step Corpus: 000269
- to stream Pmc, to step Curation: 000269
- to stream Pmc, to step Checkpoint: 000814
- to stream PubMed, to step Corpus: 000B01
- to stream PubMed, to step Curation: 000B01
- to stream PubMed, to step Checkpoint: 000C50
- to stream Ncbi, to step Merge: 001C32
- to stream Ncbi, to step Curation: 001C32
- to stream Ncbi, to step Checkpoint: 001C32
- to stream Main, to step Merge: 000D29
- to stream Main, to step Curation: 000D26
Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">K-mer clustering algorithm using a MapReduce framework: application to the parallelization of the Inchworm module of Trinity</title><author><name sortKey="Kim, Chang Sik" sort="Kim, Chang Sik" uniqKey="Kim C" first="Chang Sik" last="Kim">Chang Sik Kim</name><affiliation><nlm:aff id="Aff1"><institution-wrap><institution-id institution-id-type="ISNI">0000 0001 0727 2226</institution-id><institution-id institution-id-type="GRID">grid.482271.a</institution-id><institution>The Hartree Centre and Scientific Computing Department, STFC Daresbury Laboratory,</institution></institution-wrap>Warrington, WA4 4AD UK</nlm:aff><wicri:noCountry code="subfield">WA4 4AD UK</wicri:noCountry></affiliation><affiliation wicri:level="3"><nlm:aff id="Aff3"><institution-wrap><institution-id institution-id-type="ISNI">0000000121662407</institution-id><institution-id institution-id-type="GRID">grid.5379.8</institution-id><institution>Present addresse Cancer Research UK Manchester Institute, The University of Manchester,</institution></institution-wrap>M20 4BX, Manchester, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>M20 4BX, Manchester</wicri:regionArea><placeName><settlement type="city">Manchester</settlement><region type="country">Angleterre</region><region type="région" nuts="1">Grand Manchester</region></placeName></affiliation></author><author><name sortKey="Winn, Martyn D" sort="Winn, Martyn D" uniqKey="Winn M" first="Martyn D." last="Winn">Martyn D. Winn</name><affiliation><nlm:aff id="Aff1"><institution-wrap><institution-id institution-id-type="ISNI">0000 0001 0727 2226</institution-id><institution-id institution-id-type="GRID">grid.482271.a</institution-id><institution>The Hartree Centre and Scientific Computing Department, STFC Daresbury Laboratory,</institution></institution-wrap>Warrington, WA4 4AD UK</nlm:aff><wicri:noCountry code="subfield">WA4 4AD UK</wicri:noCountry></affiliation></author><author><name sortKey="Sachdeva, Vipin" sort="Sachdeva, Vipin" uniqKey="Sachdeva V" first="Vipin" last="Sachdeva">Vipin Sachdeva</name><affiliation wicri:level="2"><nlm:aff id="Aff2">Computational Science Center, IBM T.J. Watson Research, Cambridge, MA USA</nlm:aff><country>États-Unis</country><placeName><region type="state">Massachusetts</region></placeName><wicri:cityArea>Computational Science Center, IBM T.J. Watson Research, Cambridge</wicri:cityArea></affiliation><affiliation wicri:level="2"><nlm:aff id="Aff4">Present addresse Silicon Therapeutics, 300 A Street, Boston, MA USA</nlm:aff><country>États-Unis</country><placeName><region type="state">Massachusetts</region></placeName><wicri:cityArea>Present addresse Silicon Therapeutics, 300 A Street, Boston</wicri:cityArea></affiliation></author><author><name sortKey="Jordan, Kirk E" sort="Jordan, Kirk E" uniqKey="Jordan K" first="Kirk E." last="Jordan">Kirk E. Jordan</name><affiliation wicri:level="2"><nlm:aff id="Aff2">Computational Science Center, IBM T.J. Watson Research, Cambridge, MA USA</nlm:aff><country>États-Unis</country><placeName><region type="state">Massachusetts</region></placeName><wicri:cityArea>Computational Science Center, IBM T.J. Watson Research, Cambridge</wicri:cityArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">29100493</idno><idno type="pmc">5670514</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5670514</idno><idno type="RBID">PMC:5670514</idno><idno type="doi">10.1186/s12859-017-1881-8</idno><date when="2017">2017</date><idno type="wicri:Area/Pmc/Corpus">000269</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000269</idno><idno type="wicri:Area/Pmc/Curation">000269</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000269</idno><idno type="wicri:Area/Pmc/Checkpoint">000814</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">000814</idno><idno type="wicri:source">PubMed</idno><idno type="RBID">pubmed:29100493</idno><idno type="wicri:Area/PubMed/Corpus">000B01</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000B01</idno><idno type="wicri:Area/PubMed/Curation">000B01</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">000B01</idno><idno type="wicri:Area/PubMed/Checkpoint">000C50</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">000C50</idno><idno type="wicri:Area/Ncbi/Merge">001C32</idno><idno type="wicri:Area/Ncbi/Curation">001C32</idno><idno type="wicri:Area/Ncbi/Checkpoint">001C32</idno><idno type="wicri:Area/Main/Merge">000D29</idno><idno type="wicri:Area/Main/Curation">000D26</idno><idno type="wicri:Area/Main/Exploration">000D26</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">K-mer clustering algorithm using a MapReduce framework: application to the parallelization of the Inchworm module of Trinity</title><author><name sortKey="Kim, Chang Sik" sort="Kim, Chang Sik" uniqKey="Kim C" first="Chang Sik" last="Kim">Chang Sik Kim</name><affiliation><nlm:aff id="Aff1"><institution-wrap><institution-id institution-id-type="ISNI">0000 0001 0727 2226</institution-id><institution-id institution-id-type="GRID">grid.482271.a</institution-id><institution>The Hartree Centre and Scientific Computing Department, STFC Daresbury Laboratory,</institution></institution-wrap>Warrington, WA4 4AD UK</nlm:aff><wicri:noCountry code="subfield">WA4 4AD UK</wicri:noCountry></affiliation><affiliation wicri:level="3"><nlm:aff id="Aff3"><institution-wrap><institution-id institution-id-type="ISNI">0000000121662407</institution-id><institution-id institution-id-type="GRID">grid.5379.8</institution-id><institution>Present addresse Cancer Research UK Manchester Institute, The University of Manchester,</institution></institution-wrap>M20 4BX, Manchester, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>M20 4BX, Manchester</wicri:regionArea><placeName><settlement type="city">Manchester</settlement><region type="country">Angleterre</region><region type="région" nuts="1">Grand Manchester</region></placeName></affiliation></author><author><name sortKey="Winn, Martyn D" sort="Winn, Martyn D" uniqKey="Winn M" first="Martyn D." last="Winn">Martyn D. Winn</name><affiliation><nlm:aff id="Aff1"><institution-wrap><institution-id institution-id-type="ISNI">0000 0001 0727 2226</institution-id><institution-id institution-id-type="GRID">grid.482271.a</institution-id><institution>The Hartree Centre and Scientific Computing Department, STFC Daresbury Laboratory,</institution></institution-wrap>Warrington, WA4 4AD UK</nlm:aff><wicri:noCountry code="subfield">WA4 4AD UK</wicri:noCountry></affiliation></author><author><name sortKey="Sachdeva, Vipin" sort="Sachdeva, Vipin" uniqKey="Sachdeva V" first="Vipin" last="Sachdeva">Vipin Sachdeva</name><affiliation wicri:level="2"><nlm:aff id="Aff2">Computational Science Center, IBM T.J. Watson Research, Cambridge, MA USA</nlm:aff><country>États-Unis</country><placeName><region type="state">Massachusetts</region></placeName><wicri:cityArea>Computational Science Center, IBM T.J. Watson Research, Cambridge</wicri:cityArea></affiliation><affiliation wicri:level="2"><nlm:aff id="Aff4">Present addresse Silicon Therapeutics, 300 A Street, Boston, MA USA</nlm:aff><country>États-Unis</country><placeName><region type="state">Massachusetts</region></placeName><wicri:cityArea>Present addresse Silicon Therapeutics, 300 A Street, Boston</wicri:cityArea></affiliation></author><author><name sortKey="Jordan, Kirk E" sort="Jordan, Kirk E" uniqKey="Jordan K" first="Kirk E." last="Jordan">Kirk E. Jordan</name><affiliation wicri:level="2"><nlm:aff id="Aff2">Computational Science Center, IBM T.J. Watson Research, Cambridge, MA USA</nlm:aff><country>États-Unis</country><placeName><region type="state">Massachusetts</region></placeName><wicri:cityArea>Computational Science Center, IBM T.J. Watson Research, Cambridge</wicri:cityArea></affiliation></author></analytic><series><title level="j">BMC Bioinformatics</title><idno type="eISSN">1471-2105</idno><imprint><date when="2017">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term><term>Cluster Analysis</term><term>High-Throughput Nucleotide Sequencing</term><term>RNA (chemistry)</term><term>RNA (genetics)</term><term>Sequence Analysis, RNA</term><term>Transcriptome</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ARN ()</term><term>ARN (génétique)</term><term>Algorithmes</term><term>Analyse de regroupements</term><term>Analyse de séquence d'ARN</term><term>Séquençage nucléotidique à haut débit</term><term>Transcriptome</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>RNA</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>RNA</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ARN</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Cluster Analysis</term><term>High-Throughput Nucleotide Sequencing</term><term>Sequence Analysis, RNA</term><term>Transcriptome</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>ARN</term><term>Algorithmes</term><term>Analyse de regroupements</term><term>Analyse de séquence d'ARN</term><term>Séquençage nucléotidique à haut débit</term><term>Transcriptome</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p id="Par1">De novo transcriptome assembly is an important technique for understanding gene expression in non-model organisms. Many de novo assemblers using the de Bruijn graph of a set of the RNA sequences rely on in-memory representation of this graph. However, current methods analyse the complete set of read-derived k-mer sequence at once, resulting in the need for computer hardware with large shared memory.</p></sec><sec><title>Results</title><p id="Par2">We introduce a novel approach that clusters k-mers as the first step. The clusters correspond to small sets of gene products, which can be processed quickly to give candidate transcripts. We implement the clustering step using the MapReduce approach for parallelising the analysis of large datasets, which enables the use of compute clusters. The computational task is distributed across the compute system using the industry-standard MPI protocol, and no specialised hardware is required. Using this approach, we have re-implemented the Inchworm module from the widely used Trinity pipeline, and tested the method in the context of the full Trinity pipeline. Validation tests on a range of real datasets show large reductions in the runtime and per-node memory requirements, when making use of a compute cluster.</p></sec><sec><title>Conclusions</title><p id="Par3">Our study shows that MapReduce-based clustering has great potential for distributing challenging sequencing problems, without loss of accuracy. Although we have focussed on the Trinity package, we propose that such clustering is a useful initial step for other assembly pipelines.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (10.1186/s12859-017-1881-8) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Corney, Dc" uniqKey="Corney D">DC Corney</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Schliesky, S" uniqKey="Schliesky S">S Schliesky</name></author><author><name sortKey="Gowik, U" uniqKey="Gowik U">U Gowik</name></author><author><name sortKey="Weber, Apm" uniqKey="Weber A">APM Weber</name></author><author><name sortKey="Brautigam, A" uniqKey="Brautigam A">A Brautigam</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Oshlack, A" uniqKey="Oshlack A">A Oshlack</name></author><author><name sortKey="Robinson, Md" uniqKey="Robinson M">MD Robinson</name></author><author><name sortKey="Young, Md" uniqKey="Young M">MD Young</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gunaratne, Ph" uniqKey="Gunaratne P">PH Gunaratne</name></author><author><name sortKey="Coarfa, C" uniqKey="Coarfa C">C Coarfa</name></author><author><name sortKey="Soibam, B" uniqKey="Soibam B">B Soibam</name></author><author><name sortKey="Tandon, A" uniqKey="Tandon A">A Tandon</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ulitsky, I" uniqKey="Ulitsky I">I Ulitsky</name></author><author><name sortKey="Bartel, Dp" uniqKey="Bartel D">DP Bartel</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Memczak, S" uniqKey="Memczak S">S Memczak</name></author><author><name sortKey="Jens, M" uniqKey="Jens M">M Jens</name></author><author><name sortKey="Elefsinioti, A" uniqKey="Elefsinioti A">A Elefsinioti</name></author><author><name sortKey="Torti, F" uniqKey="Torti F">F Torti</name></author><author><name sortKey="Krueger, J" uniqKey="Krueger J">J Krueger</name></author><author><name sortKey="Rybak, A" uniqKey="Rybak A">A Rybak</name></author><author><name sortKey="Maier, L" uniqKey="Maier L">L Maier</name></author><author><name sortKey="Mackowiak, Sd" uniqKey="Mackowiak S">SD Mackowiak</name></author><author><name sortKey="Gregersen, Lh" uniqKey="Gregersen L">LH Gregersen</name></author><author><name sortKey="Munschauer, M" uniqKey="Munschauer M">M Munschauer</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Morin, Rd" uniqKey="Morin R">RD Morin</name></author><author><name sortKey="Bainbridge, M" uniqKey="Bainbridge M">M Bainbridge</name></author><author><name sortKey="Fejes, A" uniqKey="Fejes A">A Fejes</name></author><author><name sortKey="Hirst, M" uniqKey="Hirst M">M Hirst</name></author><author><name sortKey="Krzywinski, M" uniqKey="Krzywinski M">M Krzywinski</name></author><author><name sortKey="Pugh, Tj" uniqKey="Pugh T">TJ Pugh</name></author><author><name sortKey="Mcdonald, H" uniqKey="Mcdonald H">H McDonald</name></author><author><name sortKey="Varhol, R" uniqKey="Varhol R">R Varhol</name></author><author><name sortKey="Jones, Sjm" uniqKey="Jones S">SJM Jones</name></author><author><name sortKey="Marra, Ma" uniqKey="Marra M">MA Marra</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wang, Et" uniqKey="Wang E">ET Wang</name></author><author><name sortKey="Sandberg, R" uniqKey="Sandberg R">R Sandberg</name></author><author><name sortKey="Luo, S" uniqKey="Luo S">S Luo</name></author><author><name sortKey="Khrebtukova, I" uniqKey="Khrebtukova I">I Khrebtukova</name></author><author><name sortKey="Zhang, L" uniqKey="Zhang L">L Zhang</name></author><author><name sortKey="Mayr, C" uniqKey="Mayr C">C Mayr</name></author><author><name sortKey="Kingsmore, Sf" uniqKey="Kingsmore S">SF Kingsmore</name></author><author><name sortKey="Schroth, Gp" uniqKey="Schroth G">GP Schroth</name></author><author><name sortKey="Burge, Cb" uniqKey="Burge C">CB Burge</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Fullwood, Mj" uniqKey="Fullwood M">MJ Fullwood</name></author><author><name sortKey="Wei, C L" uniqKey="Wei C">C-L Wei</name></author><author><name sortKey="Liu, Et" uniqKey="Liu E">ET Liu</name></author><author><name sortKey="Ruan, Y" uniqKey="Ruan Y">Y Ruan</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yassour, M" uniqKey="Yassour M">M Yassour</name></author><author><name sortKey="Kaplan, T" uniqKey="Kaplan T">T Kaplan</name></author><author><name sortKey="Fraser, Hb" uniqKey="Fraser H">HB Fraser</name></author><author><name sortKey="Levin, Jz" uniqKey="Levin J">JZ Levin</name></author><author><name sortKey="Pfiffner, J" uniqKey="Pfiffner J">J Pfiffner</name></author><author><name sortKey="Adiconis, X" uniqKey="Adiconis X">X Adiconis</name></author><author><name sortKey="Schroth, G" uniqKey="Schroth G">G Schroth</name></author><author><name sortKey="Luo, S" uniqKey="Luo S">S Luo</name></author><author><name sortKey="Khrebtukova, I" uniqKey="Khrebtukova I">I Khrebtukova</name></author><author><name sortKey="Gnirke, A" uniqKey="Gnirke A">A Gnirke</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Guttman, M" uniqKey="Guttman M">M Guttman</name></author><author><name sortKey="Garber, M" uniqKey="Garber M">M Garber</name></author><author><name sortKey="Levin, Jz" uniqKey="Levin J">JZ Levin</name></author><author><name sortKey="Donaghey, J" uniqKey="Donaghey J">J Donaghey</name></author><author><name sortKey="Robinson, J" uniqKey="Robinson J">J Robinson</name></author><author><name sortKey="Adiconis, X" uniqKey="Adiconis X">X Adiconis</name></author><author><name sortKey="Fan, L" uniqKey="Fan L">L Fan</name></author><author><name sortKey="Koziol, Mj" uniqKey="Koziol M">MJ Koziol</name></author><author><name sortKey="Gnirke, A" uniqKey="Gnirke A">A Gnirke</name></author><author><name sortKey="Nusbaum, C" uniqKey="Nusbaum C">C Nusbaum</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Trapnell, C" uniqKey="Trapnell C">C Trapnell</name></author><author><name sortKey="Williams, Ba" uniqKey="Williams B">BA Williams</name></author><author><name sortKey="Pertea, G" uniqKey="Pertea G">G Pertea</name></author><author><name sortKey="Mortazavi, A" uniqKey="Mortazavi A">A Mortazavi</name></author><author><name sortKey="Kwan, G" uniqKey="Kwan G">G Kwan</name></author><author><name sortKey="Van Baren, Mj" uniqKey="Van Baren M">MJ van Baren</name></author><author><name sortKey="Salzberg, Sl" uniqKey="Salzberg S">SL Salzberg</name></author><author><name sortKey="Wold, Bj" uniqKey="Wold B">BJ Wold</name></author><author><name sortKey="Pachter, L" uniqKey="Pachter L">L Pachter</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Schulz, Mh" uniqKey="Schulz M">MH Schulz</name></author><author><name sortKey="Zerbino, Dr" uniqKey="Zerbino D">DR Zerbino</name></author><author><name sortKey="Vingron, M" uniqKey="Vingron M">M Vingron</name></author><author><name sortKey="Birney, E" uniqKey="Birney E">E Birney</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sze, S H" uniqKey="Sze S">S-H Sze</name></author><author><name sortKey="Tarone, Am" uniqKey="Tarone A">AM Tarone</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zerbino, Dr" uniqKey="Zerbino D">DR Zerbino</name></author><author><name sortKey="Birney, E" uniqKey="Birney E">E Birney</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Birol, I" uniqKey="Birol I">I Birol</name></author><author><name sortKey="Jackman, Sd" uniqKey="Jackman S">SD Jackman</name></author><author><name sortKey="Nielsen, Cb" uniqKey="Nielsen C">CB Nielsen</name></author><author><name sortKey="Qian, Jq" uniqKey="Qian J">JQ Qian</name></author><author><name sortKey="Varhol, R" uniqKey="Varhol R">R Varhol</name></author><author><name sortKey="Stazyk, G" uniqKey="Stazyk G">G Stazyk</name></author><author><name sortKey="Morin, Rd" uniqKey="Morin R">RD Morin</name></author><author><name sortKey="Zhao, Y" uniqKey="Zhao Y">Y Zhao</name></author><author><name sortKey="Hirst, M" uniqKey="Hirst M">M Hirst</name></author><author><name sortKey="Schein, Je" uniqKey="Schein J">JE Schein</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Simpson, Jt" uniqKey="Simpson J">JT Simpson</name></author><author><name sortKey="Wong, K" uniqKey="Wong K">K Wong</name></author><author><name sortKey="Jackman, Sd" uniqKey="Jackman S">SD Jackman</name></author><author><name sortKey="Schein, Je" uniqKey="Schein J">JE Schein</name></author><author><name sortKey="Jones, Sjm" uniqKey="Jones S">SJM Jones</name></author><author><name sortKey="Birol, I" uniqKey="Birol I">I Birol</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Xie, Y" uniqKey="Xie Y">Y Xie</name></author><author><name sortKey="Wu, G" uniqKey="Wu G">G Wu</name></author><author><name sortKey="Tang, J" uniqKey="Tang J">J Tang</name></author><author><name sortKey="Luo, R" uniqKey="Luo R">R Luo</name></author><author><name sortKey="Patterson, J" uniqKey="Patterson J">J Patterson</name></author><author><name sortKey="Liu, S" uniqKey="Liu S">S Liu</name></author><author><name sortKey="Huang, W" uniqKey="Huang W">W Huang</name></author><author><name sortKey="He, G" uniqKey="He G">G He</name></author><author><name sortKey="Gu, S" uniqKey="Gu S">S Gu</name></author><author><name sortKey="Li, S" uniqKey="Li S">S Li</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Li, R" uniqKey="Li R">R Li</name></author><author><name sortKey="Zhu, H" uniqKey="Zhu H">H Zhu</name></author><author><name sortKey="Ruan, J" uniqKey="Ruan J">J Ruan</name></author><author><name sortKey="Qian, W" uniqKey="Qian W">W Qian</name></author><author><name sortKey="Fang, X" uniqKey="Fang X">X Fang</name></author><author><name sortKey="Shi, Z" uniqKey="Shi Z">Z Shi</name></author><author><name sortKey="Li, Y" uniqKey="Li Y">Y Li</name></author><author><name sortKey="Li, S" uniqKey="Li S">S Li</name></author><author><name sortKey="Shan, G" uniqKey="Shan G">G Shan</name></author><author><name sortKey="Kristiansen, K" uniqKey="Kristiansen K">K Kristiansen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Grabherr, Mg" uniqKey="Grabherr M">MG Grabherr</name></author><author><name sortKey="Haas, Bj" uniqKey="Haas B">BJ Haas</name></author><author><name sortKey="Yassour, M" uniqKey="Yassour M">M Yassour</name></author><author><name sortKey="Levin, Jz" uniqKey="Levin J">JZ Levin</name></author><author><name sortKey="Thompson, Da" uniqKey="Thompson D">DA Thompson</name></author><author><name sortKey="Amit, I" uniqKey="Amit I">I Amit</name></author><author><name sortKey="Adiconis, X" uniqKey="Adiconis X">X Adiconis</name></author><author><name sortKey="Fan, L" uniqKey="Fan L">L Fan</name></author><author><name sortKey="Raychowdhury, R" uniqKey="Raychowdhury R">R Raychowdhury</name></author><author><name sortKey="Zeng, Q" uniqKey="Zeng Q">Q Zeng</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Liu, J" uniqKey="Liu J">J Liu</name></author><author><name sortKey="Li, G" uniqKey="Li G">G Li</name></author><author><name sortKey="Chang, Z" uniqKey="Chang Z">Z Chang</name></author><author><name sortKey="Yu, T" uniqKey="Yu T">T Yu</name></author><author><name sortKey="Liu, B" uniqKey="Liu B">B Liu</name></author><author><name sortKey="Mcmullen, R" uniqKey="Mcmullen R">R McMullen</name></author><author><name sortKey="Chen, P" uniqKey="Chen P">P Chen</name></author><author><name sortKey="Huang, X" uniqKey="Huang X">X Huang</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Zhao, Q Y" uniqKey="Zhao Q">Q-Y Zhao</name></author><author><name sortKey="Wang, Y" uniqKey="Wang Y">Y Wang</name></author><author><name sortKey="Kong, Y M" uniqKey="Kong Y">Y-M Kong</name></author><author><name sortKey="Luo, D" uniqKey="Luo D">D Luo</name></author><author><name sortKey="Li, X" uniqKey="Li X">X Li</name></author><author><name sortKey="Hao, P" uniqKey="Hao P">P Hao</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sachdeva, V" uniqKey="Sachdeva V">V Sachdeva</name></author><author><name sortKey="Kim, Cs" uniqKey="Kim C">CS Kim</name></author><author><name sortKey="Jordan, Ke" uniqKey="Jordan K">KE Jordan</name></author><author><name sortKey="Winn, Md" uniqKey="Winn M">MD Winn</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Brown, Ct" uniqKey="Brown C">CT Brown</name></author><author><name sortKey="Howe, A" uniqKey="Howe A">A Howe</name></author><author><name sortKey="Zhang, Q" uniqKey="Zhang Q">Q Zhang</name></author><author><name sortKey="Pyrkosz, Ab" uniqKey="Pyrkosz A">AB Pyrkosz</name></author><author><name sortKey="Brom, Th" uniqKey="Brom T">TH Brom</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Dean, J" uniqKey="Dean J">J Dean</name></author><author><name sortKey="Ghemawat, S" uniqKey="Ghemawat S">S Ghemawat</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mckenna, A" uniqKey="Mckenna A">A McKenna</name></author><author><name sortKey="Hanna, M" uniqKey="Hanna M">M Hanna</name></author><author><name sortKey="Banks, E" uniqKey="Banks E">E Banks</name></author><author><name sortKey="Sivachenko, A" uniqKey="Sivachenko A">A Sivachenko</name></author><author><name sortKey="Kristian Cibulskis, Ak" uniqKey="Kristian Cibulskis A">AK Kristian Cibulskis</name></author><author><name sortKey="Garimella, K" uniqKey="Garimella K">K Garimella</name></author><author><name sortKey="Altshuler, D" uniqKey="Altshuler D">D Altshuler</name></author><author><name sortKey="Gabriel, S" uniqKey="Gabriel S">S Gabriel</name></author><author><name sortKey="Daly, M" uniqKey="Daly M">M Daly</name></author><author><name sortKey="Depristo, Ma" uniqKey="Depristo M">MA DePristo</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mohammed, Ea" uniqKey="Mohammed E">EA Mohammed</name></author><author><name sortKey="Far, Bh" uniqKey="Far B">BH Far</name></author><author><name sortKey="Naugler, C" uniqKey="Naugler C">C Naugler</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Xu, B" uniqKey="Xu B">B Xu</name></author><author><name sortKey="Gao, J" uniqKey="Gao J">J Gao</name></author><author><name sortKey="Li, C" uniqKey="Li C">C Li</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Hopcroft, Je" uniqKey="Hopcroft J">JE Hopcroft</name></author><author><name sortKey="Tarjan, Re" uniqKey="Tarjan R">RE Tarjan</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Plimpton, Sj" uniqKey="Plimpton S">SJ Plimpton</name></author><author><name sortKey="Devine, Kd" uniqKey="Devine K">KD Devine</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Li, B" uniqKey="Li B">B Li</name></author><author><name sortKey="Ruotti, V" uniqKey="Ruotti V">V Ruotti</name></author><author><name sortKey="Stewart, Rm" uniqKey="Stewart R">RM Stewart</name></author><author><name sortKey="Thomson, Ja" uniqKey="Thomson J">JA Thomson</name></author><author><name sortKey="Dewey, Cn" uniqKey="Dewey C">CN Dewey</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Li, B" uniqKey="Li B">B Li</name></author><author><name sortKey="Fillmore, N" uniqKey="Fillmore N">N Fillmore</name></author><author><name sortKey="Bai, Y" uniqKey="Bai Y">Y Bai</name></author><author><name sortKey="Collins, M" uniqKey="Collins M">M Collins</name></author><author><name sortKey="Thomson, Ja" uniqKey="Thomson J">JA Thomson</name></author><author><name sortKey="Stewart, R" uniqKey="Stewart R">R Stewart</name></author><author><name sortKey="Dewey, C" uniqKey="Dewey C">C Dewey</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kent, Wj" uniqKey="Kent W">WJ Kent</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Pedersen, Bs" uniqKey="Pedersen B">BS Pedersen</name></author><author><name sortKey="Yang, Iv" uniqKey="Yang I">IV Yang</name></author><author><name sortKey="De, S" uniqKey="De S">S De</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Marcais, G" uniqKey="Marcais G">G Marcais</name></author><author><name sortKey="Kingsford, C" uniqKey="Kingsford C">C Kingsford</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Pell, J" uniqKey="Pell J">J Pell</name></author><author><name sortKey="Hintze, A" uniqKey="Hintze A">A Hintze</name></author><author><name sortKey="Canino Koning, R" uniqKey="Canino Koning R">R Canino-Koning</name></author><author><name sortKey="Howe, A" uniqKey="Howe A">A Howe</name></author><author><name sortKey="Tiedje, Jm" uniqKey="Tiedje J">JM Tiedje</name></author><author><name sortKey="Brown, Ct" uniqKey="Brown C">CT Brown</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Peng, Y" uniqKey="Peng Y">Y Peng</name></author><author><name sortKey="Leung, Hcm" uniqKey="Leung H">HCM Leung</name></author><author><name sortKey="Yiu, Sm" uniqKey="Yiu S">SM Yiu</name></author><author><name sortKey="Chin, Fyl" uniqKey="Chin F">FYL Chin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Leung, Hcm" uniqKey="Leung H">HCM Leung</name></author><author><name sortKey="Yiu, Sm" uniqKey="Yiu S">SM Yiu</name></author><author><name sortKey="Parkinson, J" uniqKey="Parkinson J">J Parkinson</name></author><author><name sortKey="Chin, Fyl" uniqKey="Chin F">FYL Chin</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Royaume-Uni</li><li>États-Unis</li></country><region><li>Angleterre</li><li>Grand Manchester</li><li>Massachusetts</li></region><settlement><li>Manchester</li></settlement></list><tree><noCountry><name sortKey="Winn, Martyn D" sort="Winn, Martyn D" uniqKey="Winn M" first="Martyn D." last="Winn">Martyn D. Winn</name></noCountry><country name="Royaume-Uni"><region name="Angleterre"><name sortKey="Kim, Chang Sik" sort="Kim, Chang Sik" uniqKey="Kim C" first="Chang Sik" last="Kim">Chang Sik Kim</name></region></country><country name="États-Unis"><region name="Massachusetts"><name sortKey="Sachdeva, Vipin" sort="Sachdeva, Vipin" uniqKey="Sachdeva V" first="Vipin" last="Sachdeva">Vipin Sachdeva</name></region><name sortKey="Jordan, Kirk E" sort="Jordan, Kirk E" uniqKey="Jordan K" first="Kirk E." last="Jordan">Kirk E. Jordan</name><name sortKey="Sachdeva, Vipin" sort="Sachdeva, Vipin" uniqKey="Sachdeva V" first="Vipin" last="Sachdeva">Vipin Sachdeva</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/Main/Exploration
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000D26 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 000D26 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Sante
|area= MersV1
|flux= Main
|étape= Exploration
|type= RBID
|clé= PMC:5670514
|texte= K-mer clustering algorithm using a MapReduce framework: application to the parallelization of the Inchworm module of Trinity
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:29100493" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \
| NlmPubMed2Wicri -a MersV1
| This area was generated with Dilib version V0.6.33. |  |