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MetCap: a bioinformatics probe design pipeline for large-scale targeted metagenomics

Kushwaha, Sandeep LU ; Manoharan, Lokeshwaran LU ; Meerupati, Tejashwari LU ; Hedlund, Katarina LU and Ahrén, Dag LU (2015) In BMC Bioinformatics 16.
Abstract
Background: Massive sequencing of genes from different environments has evolved metagenomics as central to enhancing the understanding of the wide diversity of micro-organisms and their roles in driving ecological processes. Reduced cost and high throughput sequencing has made large-scale projects achievable to a wider group of researchers, though complete metagenome sequencing is still a daunting task in terms of sequencing as well as the downstream bioinformatics analyses. Alternative approaches such as targeted amplicon sequencing requires custom PCR primer generation, and is not scalable to thousands of genes or gene families. Results: In this study, we are presenting a web-based tool called MetCap that circumvents the limitations of... (More)
Background: Massive sequencing of genes from different environments has evolved metagenomics as central to enhancing the understanding of the wide diversity of micro-organisms and their roles in driving ecological processes. Reduced cost and high throughput sequencing has made large-scale projects achievable to a wider group of researchers, though complete metagenome sequencing is still a daunting task in terms of sequencing as well as the downstream bioinformatics analyses. Alternative approaches such as targeted amplicon sequencing requires custom PCR primer generation, and is not scalable to thousands of genes or gene families. Results: In this study, we are presenting a web-based tool called MetCap that circumvents the limitations of amplicon sequencing of multiple genes by designing probes that are suitable for large-scale targeted metagenomics sequencing studies. MetCap provides a novel approach to target thousands of genes and genomic regions that could be used in targeted metagenomics studies. Automatic analysis of user-defined sequences is performed, and probes specifically designed for metagenome studies are generated. To illustrate the advantage of a targeted metagenome approach, we have generated more than 300,000 probes that match more than 400,000 publicly available sequences related to carbon degradation, and used these probes for target sequencing in a soil metagenome study. The results show high enrichment of target genes and a successful capturing of the majority of gene families. MetCap is freely available to users from: http://soilecology.biol.lu.se/metcap/. Conclusion: MetCap is facilitating probe-based target enrichment as an easy and efficient alternative tool compared to complex primer-based enrichment for large-scale investigations of metagenomes. Our results have shown efficient large-scale target enrichment through MetCap-designed probes for a soil metagenome. The web service is suitable for any targeted metagenomics project that aims to study several genes simultaneously. The novel bioinformatics approach taken by the web service will enable researchers in microbial ecology to tap into the vast diversity of microbial communities using targeted metagenomics as a cost-effective alternative to whole metagenome sequencing. (Less)
Please use this url to cite or link to this publication:
author
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
Bioinformatics, Environmental sequencing, Functional genes, Metagenome, Probe design pipeline, Targeted metagenomics, Sequence capture, MetCap
in
BMC Bioinformatics
volume
16
publisher
BioMed Central
external identifiers
  • wos:000350619700001
  • pmid:25880302
  • scopus:84924867194
ISSN
1471-2105
DOI
10.1186/s12859-015-0501-8
language
English
LU publication?
yes
id
08325422-7df4-4b2b-b8d6-d835674ffa6a (old id 5300492)
date added to LUP
2015-04-24 12:55:21
date last changed
2017-10-01 04:09:09
@article{08325422-7df4-4b2b-b8d6-d835674ffa6a,
  abstract     = {Background: Massive sequencing of genes from different environments has evolved metagenomics as central to enhancing the understanding of the wide diversity of micro-organisms and their roles in driving ecological processes. Reduced cost and high throughput sequencing has made large-scale projects achievable to a wider group of researchers, though complete metagenome sequencing is still a daunting task in terms of sequencing as well as the downstream bioinformatics analyses. Alternative approaches such as targeted amplicon sequencing requires custom PCR primer generation, and is not scalable to thousands of genes or gene families. Results: In this study, we are presenting a web-based tool called MetCap that circumvents the limitations of amplicon sequencing of multiple genes by designing probes that are suitable for large-scale targeted metagenomics sequencing studies. MetCap provides a novel approach to target thousands of genes and genomic regions that could be used in targeted metagenomics studies. Automatic analysis of user-defined sequences is performed, and probes specifically designed for metagenome studies are generated. To illustrate the advantage of a targeted metagenome approach, we have generated more than 300,000 probes that match more than 400,000 publicly available sequences related to carbon degradation, and used these probes for target sequencing in a soil metagenome study. The results show high enrichment of target genes and a successful capturing of the majority of gene families. MetCap is freely available to users from: http://soilecology.biol.lu.se/metcap/. Conclusion: MetCap is facilitating probe-based target enrichment as an easy and efficient alternative tool compared to complex primer-based enrichment for large-scale investigations of metagenomes. Our results have shown efficient large-scale target enrichment through MetCap-designed probes for a soil metagenome. The web service is suitable for any targeted metagenomics project that aims to study several genes simultaneously. The novel bioinformatics approach taken by the web service will enable researchers in microbial ecology to tap into the vast diversity of microbial communities using targeted metagenomics as a cost-effective alternative to whole metagenome sequencing.},
  articleno    = {65},
  author       = {Kushwaha, Sandeep and Manoharan, Lokeshwaran and Meerupati, Tejashwari and Hedlund, Katarina and Ahrén, Dag},
  issn         = {1471-2105},
  keyword      = {Bioinformatics,Environmental sequencing,Functional genes,Metagenome,Probe design pipeline,Targeted metagenomics,Sequence capture,MetCap},
  language     = {eng},
  publisher    = {BioMed Central},
  series       = {BMC Bioinformatics},
  title        = {MetCap: a bioinformatics probe design pipeline for large-scale targeted metagenomics},
  url          = {http://dx.doi.org/10.1186/s12859-015-0501-8},
  volume       = {16},
  year         = {2015},
}