Dataset Information

NgsTools: methods for population genetics analyses from next-generation sequencing data.

ABSTRACT:

Summary

Next-generation sequencing technologies produce short reads that are either de novo assembled or mapped to a reference genome. Genotypes and/or single-nucleotide polymorphisms are then determined from the read composition at each site, which become the basis for many downstream analyses. However, for low sequencing depths, e.g. , there is considerable statistical uncertainty in the assignment of genotypes because of random sampling of homologous base pairs in heterozygotes and sequencing or alignment errors. Recently, several probabilistic methods have been proposed to account for this uncertainty and make accurate inferences from low quality and/or coverage sequencing data. We present ngsTools, a collection of programs to perform population genetics analyses from next-generation sequencing data. The methods implemented in these programs do not rely on single-nucleotide polymorphism or genotype calling and are particularly suitable for low sequencing depth data.

Availability

Programs included in ngsTools are implemented in C/C++ and are freely available for noncommercial use at https://github.com/mfumagalli/ngsTools.

Contact

mfumagalli82@gmail.com

Supplementary information

Supplementary materials are available at Bioinformatics online.

SUBMITTER: Fumagalli M

PROVIDER: S-EPMC4016704 | biostudies-literature | 2014 May

REPOSITORIES: biostudies-literature

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Publications

ngsTools: methods for population genetics analyses from next-generation sequencing data.

Fumagalli Matteo M Vieira Filipe G FG Linderoth Tyler T Nielsen Rasmus R

Bioinformatics (Oxford, England) 20140123 10

<h4>Summary</h4>Next-generation sequencing technologies produce short reads that are either de novo assembled or mapped to a reference genome. Genotypes and/or single-nucleotide polymorphisms are then determined from the read composition at each site, which become the basis for many downstream analyses. However, for low sequencing depths, e.g. , there is considerable statistical uncertainty in the assignment of genotypes because of random sampling of homologous base pairs in heterozygotes and se ...[more]

PMID: 24458950

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