These Are Not the K-mers You Are Looking For: Efficient Online K-mer Counting Using a Probabilistic Data Structure
Identifieur interne : 001A48 ( Main/Exploration ); précédent : 001A47; suivant : 001A49These Are Not the K-mers You Are Looking For: Efficient Online K-mer Counting Using a Probabilistic Data Structure
Auteurs : Qingpeng Zhang [États-Unis] ; Jason Pell [États-Unis] ; Rosangela Canino-Koning [États-Unis] ; Adina Chuang Howe [États-Unis] ; C. Titus Brown [États-Unis]Source :
- PLoS ONE [ 1932-6203 ] ; 2014.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical : Nucleotides.
- Algorithms, Computational Biology, Humans, Sequence Analysis, DNA, Software.
Abstract
K-mer abundance analysis is widely used for many purposes in nucleotide sequence analysis, including data preprocessing for de novo assembly, repeat detection, and sequencing coverage estimation. We present the khmer software package for fast and memory efficient
Url:
DOI: 10.1371/journal.pone.0101271
PubMed: 25062443
PubMed Central: 4111482
Affiliations:
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Structure</title><author><name sortKey="Zhang, Qingpeng" sort="Zhang, Qingpeng" uniqKey="Zhang Q" first="Qingpeng" last="Zhang">Qingpeng Zhang</name><affiliation wicri:level="4"><nlm:aff id="aff1"><addr-line>Department of Computer Science and Engineering, Michigan State University, East Lansing, Michigan, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Computer Science and Engineering, Michigan State University, East Lansing, Michigan</wicri:regionArea><placeName><region type="state">Michigan</region><settlement type="city">East Lansing</settlement></placeName><orgName type="university">Université d'État du Michigan</orgName></affiliation></author><author><name sortKey="Pell, Jason" sort="Pell, Jason" uniqKey="Pell J" first="Jason" last="Pell">Jason Pell</name><affiliation wicri:level="4"><nlm:aff id="aff1"><addr-line>Department of Computer Science and Engineering, Michigan State University, East Lansing, Michigan, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Computer Science and Engineering, Michigan State University, East Lansing, Michigan</wicri:regionArea><placeName><region type="state">Michigan</region><settlement type="city">East Lansing</settlement></placeName><orgName type="university">Université d'État du Michigan</orgName></affiliation></author><author><name sortKey="Canino Koning, Rosangela" sort="Canino Koning, Rosangela" uniqKey="Canino Koning R" first="Rosangela" last="Canino-Koning">Rosangela Canino-Koning</name><affiliation wicri:level="4"><nlm:aff id="aff1"><addr-line>Department of Computer Science and Engineering, Michigan State University, East Lansing, Michigan, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Computer Science and Engineering, Michigan State University, East Lansing, Michigan</wicri:regionArea><placeName><region type="state">Michigan</region><settlement type="city">East Lansing</settlement></placeName><orgName type="university">Université d'État du Michigan</orgName></affiliation></author><author><name sortKey="Howe, Adina Chuang" sort="Howe, Adina Chuang" uniqKey="Howe A" first="Adina Chuang" last="Howe">Adina Chuang Howe</name><affiliation wicri:level="4"><nlm:aff id="aff2"><addr-line>Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan</wicri:regionArea><placeName><region type="state">Michigan</region><settlement type="city">East Lansing</settlement></placeName><orgName type="university">Université d'État du Michigan</orgName></affiliation><affiliation wicri:level="4"><nlm:aff id="aff3"><addr-line>Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, Michigan, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, Michigan</wicri:regionArea><placeName><region type="state">Michigan</region><settlement type="city">East Lansing</settlement></placeName><orgName type="university">Université d'État du Michigan</orgName></affiliation></author><author><name sortKey="Brown, C Titus" sort="Brown, C Titus" uniqKey="Brown C" first="C. Titus" last="Brown">C. Titus Brown</name><affiliation wicri:level="4"><nlm:aff id="aff1"><addr-line>Department of Computer Science and Engineering, Michigan State University, East Lansing, Michigan, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Computer Science and Engineering, Michigan State University, East Lansing, Michigan</wicri:regionArea><placeName><region type="state">Michigan</region><settlement type="city">East Lansing</settlement></placeName><orgName type="university">Université d'État du Michigan</orgName></affiliation><affiliation wicri:level="4"><nlm:aff id="aff2"><addr-line>Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan</wicri:regionArea><placeName><region type="state">Michigan</region><settlement type="city">East Lansing</settlement></placeName><orgName type="university">Université d'État du Michigan</orgName></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term><term>Computational Biology</term><term>Humans</term><term>Nucleotides</term><term>Sequence Analysis, DNA</term><term>Software</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Algorithmes</term><term>Analyse de séquence d'ADN</term><term>Biologie informatique</term><term>Humains</term><term>Logiciel</term><term>Nucléotides</term></keywords><keywords scheme="MESH" type="chemical" xml:lang="en"><term>Nucleotides</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Computational Biology</term><term>Humans</term><term>Sequence Analysis, DNA</term><term>Software</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Algorithmes</term><term>Analyse de séquence d'ADN</term><term>Biologie informatique</term><term>Humains</term><term>Logiciel</term><term>Nucléotides</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>K-mer abundance analysis is widely used for many purposes in nucleotide sequence analysis, including data preprocessing for de novo assembly, repeat detection, and sequencing coverage estimation. We present the khmer software package for fast and memory efficient <italic>online</italic> counting of k-mers in sequencing data sets. Unlike previous methods based on data structures such as hash tables, suffix arrays, and trie structures, khmer relies entirely on a simple probabilistic data structure, a Count-Min Sketch. The Count-Min Sketch permits online updating and retrieval of k-mer counts in memory which is necessary to support online k-mer analysis algorithms. On sparse data sets this data structure is considerably more memory efficient than any exact data structure. In exchange, the use of a Count-Min Sketch introduces a systematic overcount for k-mers; moreover, only the counts, and not the k-mers, are stored. Here we analyze the speed, the memory usage, and the miscount rate of khmer for generating k-mer frequency distributions and retrieving k-mer counts for individual k-mers. We also compare the performance of khmer to several other k-mer counting packages, including Tallymer, Jellyfish, BFCounter, DSK, KMC, Turtle and KAnalyze. Finally, we examine the effectiveness of profiling sequencing error, k-mer abundance trimming, and digital normalization of reads in the context of high khmer false positive rates. khmer is implemented in C++ wrapped in a Python interface, offers a tested and robust API, and is freely available under the BSD license at github.com/ged-lab/khmer.</p></div></front><back><div1 type="bibliography"><listBibl><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="Kurtz, S" uniqKey="Kurtz S">S Kurtz</name></author><author><name sortKey="Narechania, A" uniqKey="Narechania A">A Narechania</name></author><author><name sortKey="Stein, Jc" uniqKey="Stein J">JC Stein</name></author><author><name sortKey="Ware, D" uniqKey="Ware D">D 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Shedden</name></author><author><name sortKey="Hankenson, Kd" uniqKey="Hankenson K">KD Hankenson</name></author><author><name sortKey="Woolf, Pj" uniqKey="Woolf P">PJ Woolf</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Perez, F" uniqKey="Perez F">F Pérez</name></author><author><name sortKey="Granger, B" uniqKey="Granger B">B Granger</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Qin, J" uniqKey="Qin J">J Qin</name></author><author><name sortKey="Li, R" uniqKey="Li R">R Li</name></author><author><name sortKey="Raes, J" uniqKey="Raes J">J Raes</name></author><author><name sortKey="Arumugam, M" uniqKey="Arumugam M">M Arumugam</name></author><author><name sortKey="Burgdorf, Ks" uniqKey="Burgdorf K">KS Burgdorf</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>États-Unis</li></country><region><li>Michigan</li></region><settlement><li>East Lansing</li></settlement><orgName><li>Université d'État du Michigan</li></orgName></list><tree><country name="États-Unis"><region name="Michigan"><name sortKey="Zhang, Qingpeng" sort="Zhang, Qingpeng" uniqKey="Zhang Q" first="Qingpeng" last="Zhang">Qingpeng Zhang</name></region><name sortKey="Brown, C Titus" sort="Brown, C Titus" uniqKey="Brown C" first="C. Titus" last="Brown">C. Titus Brown</name><name sortKey="Brown, C Titus" sort="Brown, C Titus" uniqKey="Brown C" first="C. Titus" last="Brown">C. Titus Brown</name><name sortKey="Canino Koning, Rosangela" sort="Canino Koning, Rosangela" uniqKey="Canino Koning R" first="Rosangela" last="Canino-Koning">Rosangela Canino-Koning</name><name sortKey="Howe, Adina Chuang" sort="Howe, Adina Chuang" uniqKey="Howe A" first="Adina Chuang" last="Howe">Adina Chuang Howe</name><name sortKey="Howe, Adina Chuang" sort="Howe, Adina Chuang" uniqKey="Howe A" first="Adina Chuang" last="Howe">Adina Chuang Howe</name><name sortKey="Pell, Jason" sort="Pell, Jason" uniqKey="Pell J" first="Jason" last="Pell">Jason Pell</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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