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PGcloser: Fast Parallel Gap-Closing Tool Using Long-Reads or Contigs to Fill Gaps in Genomes

Assembled draft genomes usually contain many gaps because of the length limit of next-generation sequencing. Although many gap-closing tools have been developed, most of them still attempt to fill gaps on the basis of next-generation sequencing reads (always < 200 bp). Hence, the gap-filling effe...

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Autores principales: Lu, Peng, Jin, Jingjing, Li, Zefeng, Xu, Yalong, Hu, Dasha, Liu, Jiajun, Cao, Peijian
Formato: Online Artículo Texto
Lenguaje:English
Publicado: SAGE Publications 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7180314/
https://www.ncbi.nlm.nih.gov/pubmed/32362739
http://dx.doi.org/10.1177/1176934320913859
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author Lu, Peng
Jin, Jingjing
Li, Zefeng
Xu, Yalong
Hu, Dasha
Liu, Jiajun
Cao, Peijian
author_facet Lu, Peng
Jin, Jingjing
Li, Zefeng
Xu, Yalong
Hu, Dasha
Liu, Jiajun
Cao, Peijian
author_sort Lu, Peng
collection PubMed
description Assembled draft genomes usually contain many gaps because of the length limit of next-generation sequencing. Although many gap-closing tools have been developed, most of them still attempt to fill gaps on the basis of next-generation sequencing reads (always < 200 bp). Hence, the gap-filling effect is inferior. Several tools that use long-reads to close gaps have recently been created. However, they require extensive runtimes, which may not be suitable for large genomes. We describe a gap-closing tool called PGcloser, which supports parallel mode and adopts long-reads/contigs to fill gaps in genome sequences. Three tests show that PGcloser is faster than other tools but exhibits similar accuracy. PGcloser is free open-source software that is available at http://software.tobaccodb.org/software/pgcloser.
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spelling pubmed-71803142020-05-01 PGcloser: Fast Parallel Gap-Closing Tool Using Long-Reads or Contigs to Fill Gaps in Genomes Lu, Peng Jin, Jingjing Li, Zefeng Xu, Yalong Hu, Dasha Liu, Jiajun Cao, Peijian Evol Bioinform Online Parallel Computing in Evolutionary Bioinformatics Assembled draft genomes usually contain many gaps because of the length limit of next-generation sequencing. Although many gap-closing tools have been developed, most of them still attempt to fill gaps on the basis of next-generation sequencing reads (always < 200 bp). Hence, the gap-filling effect is inferior. Several tools that use long-reads to close gaps have recently been created. However, they require extensive runtimes, which may not be suitable for large genomes. We describe a gap-closing tool called PGcloser, which supports parallel mode and adopts long-reads/contigs to fill gaps in genome sequences. Three tests show that PGcloser is faster than other tools but exhibits similar accuracy. PGcloser is free open-source software that is available at http://software.tobaccodb.org/software/pgcloser. SAGE Publications 2020-04-23 /pmc/articles/PMC7180314/ /pubmed/32362739 http://dx.doi.org/10.1177/1176934320913859 Text en © The Author(s) 2020 https://creativecommons.org/licenses/by-nc/4.0/ This article is distributed under the terms of the Creative Commons Attribution-NonCommercial 4.0 License (https://creativecommons.org/licenses/by-nc/4.0/) which permits non-commercial use, reproduction and distribution of the work without further permission provided the original work is attributed as specified on the SAGE and Open Access page (https://us.sagepub.com/en-us/nam/open-access-at-sage).
spellingShingle Parallel Computing in Evolutionary Bioinformatics
Lu, Peng
Jin, Jingjing
Li, Zefeng
Xu, Yalong
Hu, Dasha
Liu, Jiajun
Cao, Peijian
PGcloser: Fast Parallel Gap-Closing Tool Using Long-Reads or Contigs to Fill Gaps in Genomes
title PGcloser: Fast Parallel Gap-Closing Tool Using Long-Reads or Contigs to Fill Gaps in Genomes
title_full PGcloser: Fast Parallel Gap-Closing Tool Using Long-Reads or Contigs to Fill Gaps in Genomes
title_fullStr PGcloser: Fast Parallel Gap-Closing Tool Using Long-Reads or Contigs to Fill Gaps in Genomes
title_full_unstemmed PGcloser: Fast Parallel Gap-Closing Tool Using Long-Reads or Contigs to Fill Gaps in Genomes
title_short PGcloser: Fast Parallel Gap-Closing Tool Using Long-Reads or Contigs to Fill Gaps in Genomes
title_sort pgcloser: fast parallel gap-closing tool using long-reads or contigs to fill gaps in genomes
topic Parallel Computing in Evolutionary Bioinformatics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7180314/
https://www.ncbi.nlm.nih.gov/pubmed/32362739
http://dx.doi.org/10.1177/1176934320913859
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