SEAL: a distributed short read mapping and duplicate removal tool

Summary: SEAL is a scalable tool for short read pair mapping and duplicate removal. It computes mappings that are consistent with those produced by BWA and removes duplicates according to the same criteria employed by Picard MarkDuplicates. On a 16-node Hadoop cluster, it is capable of processing ab...

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Detalles Bibliográficos
Autores principales: Pireddu, Luca, Leo, Simone, Zanetti, Gianluigi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2011
Materias:
Applications Note
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3137215/
https://www.ncbi.nlm.nih.gov/pubmed/21697132
http://dx.doi.org/10.1093/bioinformatics/btr325
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author Pireddu, Luca
Leo, Simone
Zanetti, Gianluigi
author_facet Pireddu, Luca
Leo, Simone
Zanetti, Gianluigi
author_sort Pireddu, Luca
collection PubMed
description Summary: SEAL is a scalable tool for short read pair mapping and duplicate removal. It computes mappings that are consistent with those produced by BWA and removes duplicates according to the same criteria employed by Picard MarkDuplicates. On a 16-node Hadoop cluster, it is capable of processing about 13 GB per hour in map+rmdup mode, while reaching a throughput of 19 GB per hour in mapping-only mode. Availability: SEAL is available online at http://biodoop-seal.sourceforge.net/. Contact: luca.pireddu@crs4.it
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spelling pubmed-31372152011-07-15 SEAL: a distributed short read mapping and duplicate removal tool Pireddu, Luca Leo, Simone Zanetti, Gianluigi Bioinformatics Applications Note Summary: SEAL is a scalable tool for short read pair mapping and duplicate removal. It computes mappings that are consistent with those produced by BWA and removes duplicates according to the same criteria employed by Picard MarkDuplicates. On a 16-node Hadoop cluster, it is capable of processing about 13 GB per hour in map+rmdup mode, while reaching a throughput of 19 GB per hour in mapping-only mode. Availability: SEAL is available online at http://biodoop-seal.sourceforge.net/. Contact: luca.pireddu@crs4.it Oxford University Press 2011-08-01 2011-06-22 /pmc/articles/PMC3137215/ /pubmed/21697132 http://dx.doi.org/10.1093/bioinformatics/btr325 Text en © The Author(s) 2011. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/2.5 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Note
Pireddu, Luca
Leo, Simone
Zanetti, Gianluigi
SEAL: a distributed short read mapping and duplicate removal tool
title SEAL: a distributed short read mapping and duplicate removal tool
title_full SEAL: a distributed short read mapping and duplicate removal tool
title_fullStr SEAL: a distributed short read mapping and duplicate removal tool
title_full_unstemmed SEAL: a distributed short read mapping and duplicate removal tool
title_short SEAL: a distributed short read mapping and duplicate removal tool
title_sort seal: a distributed short read mapping and duplicate removal tool
topic Applications Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3137215/
https://www.ncbi.nlm.nih.gov/pubmed/21697132
http://dx.doi.org/10.1093/bioinformatics/btr325
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