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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...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
SAGE Publications
2020
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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. |
format | Online Article Text |
id | pubmed-7180314 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | SAGE Publications |
record_format | MEDLINE/PubMed |
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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