Cargando…

Erratum to: An improved assembly of the loblolly pine mega-genome using long-read single-molecule sequencing

The 22-gigabase genome of loblolly pine (Pinus taeda) is one of the largest ever sequenced. The draft assembly published in 2014 was built entirely from short Illumina reads, with lengths ranging from 100 to 250 base pairs (bp). The assembly was quite fragmented, containing over 11 million contigs w...

Descripción completa

Detalles Bibliográficos
Autores principales: Zimin, Aleksey V., Stevens, Kristian A., Crepeau, Marc W., Puiu, Daniela, Wegrzyn, Jill L., Yorke, James A., Langley, Charles H., Neale, David B., Salzberg, Steven L.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5632297/
https://www.ncbi.nlm.nih.gov/pubmed/29020755
http://dx.doi.org/10.1093/gigascience/gix072
_version_ 1783269673344696320
author Zimin, Aleksey V.
Stevens, Kristian A.
Crepeau, Marc W.
Puiu, Daniela
Wegrzyn, Jill L.
Yorke, James A.
Langley, Charles H.
Neale, David B.
Salzberg, Steven L.
author_facet Zimin, Aleksey V.
Stevens, Kristian A.
Crepeau, Marc W.
Puiu, Daniela
Wegrzyn, Jill L.
Yorke, James A.
Langley, Charles H.
Neale, David B.
Salzberg, Steven L.
author_sort Zimin, Aleksey V.
collection PubMed
description The 22-gigabase genome of loblolly pine (Pinus taeda) is one of the largest ever sequenced. The draft assembly published in 2014 was built entirely from short Illumina reads, with lengths ranging from 100 to 250 base pairs (bp). The assembly was quite fragmented, containing over 11 million contigs whose weighted average (N50) size was 8206 bp. To improve this result, we generated approximately 12-fold coverage in long reads using the Single Molecule Real Time sequencing technology developed at Pacific Biosciences. We assembled the long and short reads together using the MaSuRCA mega-reads assembly algorithm, which produced a substantially better assembly, P. taeda version 2.0. The new assembly has an N50 contig size of 25 361, more than three times as large as achieved in the original assembly, and an N50 scaffold size of 107 821, 61% larger than the previous assembly.
format Online
Article
Text
id pubmed-5632297
institution National Center for Biotechnology Information
language English
publishDate 2017
publisher Oxford University Press
record_format MEDLINE/PubMed
spelling pubmed-56322972017-10-12 Erratum to: An improved assembly of the loblolly pine mega-genome using long-read single-molecule sequencing Zimin, Aleksey V. Stevens, Kristian A. Crepeau, Marc W. Puiu, Daniela Wegrzyn, Jill L. Yorke, James A. Langley, Charles H. Neale, David B. Salzberg, Steven L. Gigascience Erratum The 22-gigabase genome of loblolly pine (Pinus taeda) is one of the largest ever sequenced. The draft assembly published in 2014 was built entirely from short Illumina reads, with lengths ranging from 100 to 250 base pairs (bp). The assembly was quite fragmented, containing over 11 million contigs whose weighted average (N50) size was 8206 bp. To improve this result, we generated approximately 12-fold coverage in long reads using the Single Molecule Real Time sequencing technology developed at Pacific Biosciences. We assembled the long and short reads together using the MaSuRCA mega-reads assembly algorithm, which produced a substantially better assembly, P. taeda version 2.0. The new assembly has an N50 contig size of 25 361, more than three times as large as achieved in the original assembly, and an N50 scaffold size of 107 821, 61% larger than the previous assembly. Oxford University Press 2017-10-06 /pmc/articles/PMC5632297/ /pubmed/29020755 http://dx.doi.org/10.1093/gigascience/gix072 Text en © The Authors 2017. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Erratum
Zimin, Aleksey V.
Stevens, Kristian A.
Crepeau, Marc W.
Puiu, Daniela
Wegrzyn, Jill L.
Yorke, James A.
Langley, Charles H.
Neale, David B.
Salzberg, Steven L.
Erratum to: An improved assembly of the loblolly pine mega-genome using long-read single-molecule sequencing
title Erratum to: An improved assembly of the loblolly pine mega-genome using long-read single-molecule sequencing
title_full Erratum to: An improved assembly of the loblolly pine mega-genome using long-read single-molecule sequencing
title_fullStr Erratum to: An improved assembly of the loblolly pine mega-genome using long-read single-molecule sequencing
title_full_unstemmed Erratum to: An improved assembly of the loblolly pine mega-genome using long-read single-molecule sequencing
title_short Erratum to: An improved assembly of the loblolly pine mega-genome using long-read single-molecule sequencing
title_sort erratum to: an improved assembly of the loblolly pine mega-genome using long-read single-molecule sequencing
topic Erratum
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5632297/
https://www.ncbi.nlm.nih.gov/pubmed/29020755
http://dx.doi.org/10.1093/gigascience/gix072
work_keys_str_mv AT ziminalekseyv erratumtoanimprovedassemblyoftheloblollypinemegagenomeusinglongreadsinglemoleculesequencing
AT stevenskristiana erratumtoanimprovedassemblyoftheloblollypinemegagenomeusinglongreadsinglemoleculesequencing
AT crepeaumarcw erratumtoanimprovedassemblyoftheloblollypinemegagenomeusinglongreadsinglemoleculesequencing
AT puiudaniela erratumtoanimprovedassemblyoftheloblollypinemegagenomeusinglongreadsinglemoleculesequencing
AT wegrzynjilll erratumtoanimprovedassemblyoftheloblollypinemegagenomeusinglongreadsinglemoleculesequencing
AT yorkejamesa erratumtoanimprovedassemblyoftheloblollypinemegagenomeusinglongreadsinglemoleculesequencing
AT langleycharlesh erratumtoanimprovedassemblyoftheloblollypinemegagenomeusinglongreadsinglemoleculesequencing
AT nealedavidb erratumtoanimprovedassemblyoftheloblollypinemegagenomeusinglongreadsinglemoleculesequencing
AT salzbergstevenl erratumtoanimprovedassemblyoftheloblollypinemegagenomeusinglongreadsinglemoleculesequencing