lociNGS: a lightweight alternative for assessing suitability of next-generation loci for evolutionary analysis.
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-FA...
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2012-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC3468592?pdf=render |
| _version_ | 1819094205881909248 |
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| author | Sarah M Hird |
| author_facet | Sarah M Hird |
| author_sort | Sarah M Hird |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-21T23:23:43Z |
| format | Article |
| id | doaj.art-18f2b1cd21f64a09afcb52927ac8603b |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-21T23:23:43Z |
| publishDate | 2012-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-18f2b1cd21f64a09afcb52927ac8603b2022-12-21T18:46:42ZengPublic Library of Science (PLoS)PLoS ONE1932-62032012-01-01710e4684710.1371/journal.pone.0046847lociNGS: a lightweight alternative for assessing suitability of next-generation loci for evolutionary analysis.Sarah M HirdGenomic 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.http://europepmc.org/articles/PMC3468592?pdf=render |
| spellingShingle | Sarah M Hird lociNGS: a lightweight alternative for assessing suitability of next-generation loci for evolutionary analysis. PLoS ONE |
| title | lociNGS: a lightweight alternative for assessing suitability of next-generation loci for evolutionary analysis. |
| title_full | lociNGS: a lightweight alternative for assessing suitability of next-generation loci for evolutionary analysis. |
| title_fullStr | lociNGS: a lightweight alternative for assessing suitability of next-generation loci for evolutionary analysis. |
| title_full_unstemmed | lociNGS: a lightweight alternative for assessing suitability of next-generation loci for evolutionary analysis. |
| title_short | lociNGS: a lightweight alternative for assessing suitability of next-generation loci for evolutionary analysis. |
| title_sort | locings a lightweight alternative for assessing suitability of next generation loci for evolutionary analysis |
| url | http://europepmc.org/articles/PMC3468592?pdf=render |
| work_keys_str_mv | AT sarahmhird locingsalightweightalternativeforassessingsuitabilityofnextgenerationlociforevolutionaryanalysis |