LongISLND: in silico sequencing of lengthy and noisy datatypes

Summary: LongISLND is a software package designed to simulate sequencing data according to the characteristics of third generation, single-molecule sequencing technologies. The general software architecture is easily extendable, as demonstrated by the emulation of Pacific Biosciences (PacBio) multi-...

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Autores principales: Lau, Bayo, Mohiyuddin, Marghoob, Mu, John C., Fang, Li Tai, Bani Asadi, Narges, Dallett, Carolina, Lam, Hugo Y. K.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2016
Materias:
Applications Notes
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5167071/
https://www.ncbi.nlm.nih.gov/pubmed/27667791
http://dx.doi.org/10.1093/bioinformatics/btw602
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author Lau, Bayo
Mohiyuddin, Marghoob
Mu, John C.
Fang, Li Tai
Bani Asadi, Narges
Dallett, Carolina
Lam, Hugo Y. K.
author_facet Lau, Bayo
Mohiyuddin, Marghoob
Mu, John C.
Fang, Li Tai
Bani Asadi, Narges
Dallett, Carolina
Lam, Hugo Y. K.
author_sort Lau, Bayo
collection PubMed
description Summary: LongISLND is a software package designed to simulate sequencing data according to the characteristics of third generation, single-molecule sequencing technologies. The general software architecture is easily extendable, as demonstrated by the emulation of Pacific Biosciences (PacBio) multi-pass sequencing with P5 and P6 chemistries, producing data in FASTQ, H5, and the latest PacBio BAM format. We demonstrate its utility by downstream processing with consensus building and variant calling. Availability and Implementation: LongISLND is implemented in Java and available at http://bioinform.github.io/longislnd Contact: hugo.lam@roche.com Supplementary information: Supplementary data are available at Bioinformatics online.
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spelling pubmed-51670712016-12-20 LongISLND: in silico sequencing of lengthy and noisy datatypes Lau, Bayo Mohiyuddin, Marghoob Mu, John C. Fang, Li Tai Bani Asadi, Narges Dallett, Carolina Lam, Hugo Y. K. Bioinformatics Applications Notes Summary: LongISLND is a software package designed to simulate sequencing data according to the characteristics of third generation, single-molecule sequencing technologies. The general software architecture is easily extendable, as demonstrated by the emulation of Pacific Biosciences (PacBio) multi-pass sequencing with P5 and P6 chemistries, producing data in FASTQ, H5, and the latest PacBio BAM format. We demonstrate its utility by downstream processing with consensus building and variant calling. Availability and Implementation: LongISLND is implemented in Java and available at http://bioinform.github.io/longislnd Contact: hugo.lam@roche.com Supplementary information: Supplementary data are available at Bioinformatics online. Oxford University Press 2016-12-15 2016-09-25 /pmc/articles/PMC5167071/ /pubmed/27667791 http://dx.doi.org/10.1093/bioinformatics/btw602 Text en © The Author 2016. 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 Applications Notes
Lau, Bayo
Mohiyuddin, Marghoob
Mu, John C.
Fang, Li Tai
Bani Asadi, Narges
Dallett, Carolina
Lam, Hugo Y. K.
LongISLND: in silico sequencing of lengthy and noisy datatypes
title LongISLND: in silico sequencing of lengthy and noisy datatypes
title_full LongISLND: in silico sequencing of lengthy and noisy datatypes
title_fullStr LongISLND: in silico sequencing of lengthy and noisy datatypes
title_full_unstemmed LongISLND: in silico sequencing of lengthy and noisy datatypes
title_short LongISLND: in silico sequencing of lengthy and noisy datatypes
title_sort longislnd: in silico sequencing of lengthy and noisy datatypes
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5167071/
https://www.ncbi.nlm.nih.gov/pubmed/27667791
http://dx.doi.org/10.1093/bioinformatics/btw602
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