READSCAN: a fast and scalable pathogen discovery program with accurate genome relative abundance estimation

Summary: READSCAN is a highly scalable parallel program to identify non-host sequences (of potential pathogen origin) and estimate their genome relative abundance in high-throughput sequence datasets. READSCAN accurately classified human and viral sequences on a 20.1 million reads simulated dataset...

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Detalles Bibliográficos
Autores principales: Naeem, Raeece, Rashid, Mamoon, Pain, Arnab
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2013
Materias:
Applications Notes
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3562070/
https://www.ncbi.nlm.nih.gov/pubmed/23193222
http://dx.doi.org/10.1093/bioinformatics/bts684
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author Naeem, Raeece
Rashid, Mamoon
Pain, Arnab
author_facet Naeem, Raeece
Rashid, Mamoon
Pain, Arnab
author_sort Naeem, Raeece
collection PubMed
description Summary: READSCAN is a highly scalable parallel program to identify non-host sequences (of potential pathogen origin) and estimate their genome relative abundance in high-throughput sequence datasets. READSCAN accurately classified human and viral sequences on a 20.1 million reads simulated dataset in <27 min using a small Beowulf compute cluster with 16 nodes (Supplementary Material). Availability: http://cbrc.kaust.edu.sa/readscan Contact: arnab.pain@kaust.edu.sa or raeece.naeem@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online.
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spelling pubmed-35620702013-02-01 READSCAN: a fast and scalable pathogen discovery program with accurate genome relative abundance estimation Naeem, Raeece Rashid, Mamoon Pain, Arnab Bioinformatics Applications Notes Summary: READSCAN is a highly scalable parallel program to identify non-host sequences (of potential pathogen origin) and estimate their genome relative abundance in high-throughput sequence datasets. READSCAN accurately classified human and viral sequences on a 20.1 million reads simulated dataset in <27 min using a small Beowulf compute cluster with 16 nodes (Supplementary Material). Availability: http://cbrc.kaust.edu.sa/readscan Contact: arnab.pain@kaust.edu.sa or raeece.naeem@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online. Oxford University Press 2013-02-01 2012-11-28 /pmc/articles/PMC3562070/ /pubmed/23193222 http://dx.doi.org/10.1093/bioinformatics/bts684 Text en © The Author(s) 2012. Published by Oxford University Press. http://creativecommons.org/licenses/by/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Notes
Naeem, Raeece
Rashid, Mamoon
Pain, Arnab
READSCAN: a fast and scalable pathogen discovery program with accurate genome relative abundance estimation
title READSCAN: a fast and scalable pathogen discovery program with accurate genome relative abundance estimation
title_full READSCAN: a fast and scalable pathogen discovery program with accurate genome relative abundance estimation
title_fullStr READSCAN: a fast and scalable pathogen discovery program with accurate genome relative abundance estimation
title_full_unstemmed READSCAN: a fast and scalable pathogen discovery program with accurate genome relative abundance estimation
title_short READSCAN: a fast and scalable pathogen discovery program with accurate genome relative abundance estimation
title_sort readscan: a fast and scalable pathogen discovery program with accurate genome relative abundance estimation
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3562070/
https://www.ncbi.nlm.nih.gov/pubmed/23193222
http://dx.doi.org/10.1093/bioinformatics/bts684
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