Improving de novo Assembly Based on Read Classification.
Identifieur interne : 001F12 ( Ncbi/Curation ); précédent : 001F11; suivant : 001F13Improving de novo Assembly Based on Read Classification.
Auteurs : Xingyu Liao ; Min Li ; Junwei Luo ; You Zou ; Fang-Xiang Wu ; Yi Pan ; Feng Luo ; Jianxin WangSource :
- IEEE/ACM transactions on computational biology and bioinformatics [ 1557-9964 ]
Abstract
Due to sequencing bias, sequencing error, and repeat problems, the genome assemblies usually contain misarrangements and gaps. When tackling these problems, current assemblers commonly consider the read libraries as a whole and adopt the same strategy to deal with them. However, if we can divide reads into different categories and take different assembly strategies for different read categories, we expect to reduce the mutual effects on problems in genome assembly and facilitate to produce satisfactory assemblies. In this paper, we present a new pipeline for genome assembly based on read classification (ARC). ARC classifies reads into three categories according to the frequencies of k-mers they contain. The three categories refer to (1) low depth reads, which contain a certain low frequency k-mers and are often caused by sequencing errors or bias; (2) high depth reads, which contain a certain high frequency k-mers and usually come from repetitive regions; and (3) normal depth reads, which are the rest of reads. After read classification, an existing assembler is used to assemble different read categories separately, which is beneficial to resolve problems in the genome assembly. ARC adopts loose assembly parameters for low depth reads, and strict assembly parameters for normal depth and high depth reads. We test ARC using five datasets. The experimental results show that, assemblers combining with ARC can generate better assemblies in terms of NA50, NGA50, and genome fraction.
DOI: 10.1109/TCBB.2018.2861380
PubMed: 30059317
Links toward previous steps (curation, corpus...)
- to stream PubMed, to step Corpus: Pour aller vers cette notice dans l'étape Curation :000827
- to stream PubMed, to step Curation: Pour aller vers cette notice dans l'étape Curation :000827
- to stream PubMed, to step Checkpoint: Pour aller vers cette notice dans l'étape Curation :002968
- to stream Ncbi, to step Merge: Pour aller vers cette notice dans l'étape Curation :001F12
Links to Exploration step
pubmed:30059317Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Improving de novo Assembly Based on Read Classification.</title><author><name sortKey="Liao, Xingyu" sort="Liao, Xingyu" uniqKey="Liao X" first="Xingyu" last="Liao">Xingyu Liao</name></author><author><name sortKey="Li, Min" sort="Li, Min" uniqKey="Li M" first="Min" last="Li">Min Li</name></author><author><name sortKey="Luo, Junwei" sort="Luo, Junwei" uniqKey="Luo J" first="Junwei" last="Luo">Junwei Luo</name></author><author><name sortKey="Zou, You" sort="Zou, You" uniqKey="Zou Y" first="You" last="Zou">You Zou</name></author><author><name sortKey="Wu, Fang Xiang" sort="Wu, Fang Xiang" uniqKey="Wu F" first="Fang-Xiang" last="Wu">Fang-Xiang Wu</name></author><author><name sortKey="Pan, Yi" sort="Pan, Yi" uniqKey="Pan Y" first="Yi" last="Pan">Yi Pan</name></author><author><name sortKey="Luo, Feng" sort="Luo, Feng" uniqKey="Luo F" first="Feng" last="Luo">Feng Luo</name></author><author><name sortKey="Wang, Jianxin" sort="Wang, Jianxin" uniqKey="Wang J" first="Jianxin" last="Wang">Jianxin Wang</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="????"><PubDate><MedlineDate>2020 Jan-Feb</MedlineDate></PubDate></date><idno type="RBID">pubmed:30059317</idno><idno type="pmid">30059317</idno><idno type="doi">10.1109/TCBB.2018.2861380</idno><idno type="wicri:Area/PubMed/Corpus">000827</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000827</idno><idno type="wicri:Area/PubMed/Curation">000827</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">000827</idno><idno type="wicri:Area/PubMed/Checkpoint">002968</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">002968</idno><idno type="wicri:Area/Ncbi/Merge">001F12</idno><idno type="wicri:Area/Ncbi/Curation">001F12</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Improving de novo Assembly Based on Read Classification.</title><author><name sortKey="Liao, Xingyu" sort="Liao, Xingyu" uniqKey="Liao X" first="Xingyu" last="Liao">Xingyu Liao</name></author><author><name sortKey="Li, Min" sort="Li, Min" uniqKey="Li M" first="Min" last="Li">Min Li</name></author><author><name sortKey="Luo, Junwei" sort="Luo, Junwei" uniqKey="Luo J" first="Junwei" last="Luo">Junwei Luo</name></author><author><name sortKey="Zou, You" sort="Zou, You" uniqKey="Zou Y" first="You" last="Zou">You Zou</name></author><author><name sortKey="Wu, Fang Xiang" sort="Wu, Fang Xiang" uniqKey="Wu F" first="Fang-Xiang" last="Wu">Fang-Xiang Wu</name></author><author><name sortKey="Pan, Yi" sort="Pan, Yi" uniqKey="Pan Y" first="Yi" last="Pan">Yi Pan</name></author><author><name sortKey="Luo, Feng" sort="Luo, Feng" uniqKey="Luo F" first="Feng" last="Luo">Feng Luo</name></author><author><name sortKey="Wang, Jianxin" sort="Wang, Jianxin" uniqKey="Wang J" first="Jianxin" last="Wang">Jianxin Wang</name></author></analytic><series><title level="j">IEEE/ACM transactions on computational biology and bioinformatics</title><idno type="eISSN">1557-9964</idno></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Due to sequencing bias, sequencing error, and repeat problems, the genome assemblies usually contain misarrangements and gaps. When tackling these problems, current assemblers commonly consider the read libraries as a whole and adopt the same strategy to deal with them. However, if we can divide reads into different categories and take different assembly strategies for different read categories, we expect to reduce the mutual effects on problems in genome assembly and facilitate to produce satisfactory assemblies. In this paper, we present a new pipeline for genome assembly based on read classification (ARC). ARC classifies reads into three categories according to the frequencies of k-mers they contain. The three categories refer to (1) low depth reads, which contain a certain low frequency k-mers and are often caused by sequencing errors or bias; (2) high depth reads, which contain a certain high frequency k-mers and usually come from repetitive regions; and (3) normal depth reads, which are the rest of reads. After read classification, an existing assembler is used to assemble different read categories separately, which is beneficial to resolve problems in the genome assembly. ARC adopts loose assembly parameters for low depth reads, and strict assembly parameters for normal depth and high depth reads. We test ARC using five datasets. The experimental results show that, assemblers combining with ARC can generate better assemblies in terms of NA50, NGA50, and genome fraction.</div></front></TEI></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/Ncbi/Curation
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 001F12 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Ncbi/Curation/biblio.hfd -nk 001F12 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Sante
|area= MersV1
|flux= Ncbi
|étape= Curation
|type= RBID
|clé= pubmed:30059317
|texte= Improving de novo Assembly Based on Read Classification.
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Ncbi/Curation/RBID.i -Sk "pubmed:30059317" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Ncbi/Curation/biblio.hfd \
| NlmPubMed2Wicri -a MersV1
| This area was generated with Dilib version V0.6.33. |  |