lociNGS: a lightweight alternative for assessing suitability of next-generation loci for evolutionary analysis

PLoS One. 2012;7(10):e46847. doi: 10.1371/journal.pone.0046847. Epub 2012 Oct 10.

Abstract

Genomic enrichment methods and next-generation sequencing produce uneven coverage for the portions of the genome (the loci) they target; this information is essential for ascertaining the suitability of each locus for further analysis. lociNGS is a user-friendly accessory program that takes multi-FASTA formatted loci, next-generation sequence alignments and demographic data as input and collates, displays and outputs information about the data. Summary information includes the parameters coverage per locus, coverage per individual and number of polymorphic sites, among others. The program can output the raw sequences used to call loci from next-generation sequencing data. lociNGS also reformats subsets of loci in three commonly used formats for multi-locus phylogeographic and population genetics analyses - NEXUS, IMa2 and Migrate. lociNGS is available at https://github.com/SHird/lociNGS and is dependent on installation of MongoDB (freely available at http://www.mongodb.org/downloads). lociNGS is written in Python and is supported on MacOSX and Unix; it is distributed under a GNU General Public License.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computational Biology / methods*
  • Evolution, Molecular*
  • Genetics, Population / methods
  • Internet
  • Phylogeography / methods
  • Reproducibility of Results
  • Sequence Alignment / methods*
  • Sequence Analysis, DNA / methods
  • Software*

Grant support

This work was supported by Google Inc. through the 2011 Google Summer Of CodeTM Program (http://code.google.com/soc/). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.