Constructing linkage maps in the genomics era with MapDisto 2.0.

ABSTRACT:

Motivation

Genotyping by sequencing (GBS) generates datasets that are challenging to handle by current genetic mapping software with graphical interface. Geneticists need new user-friendly computer programs that can analyze GBS data on desktop computers. This requires improvements in computation efficiency, both in terms of speed and use of random-access memory (RAM).

Results

MapDisto v.2.0 is a user-friendly computer program for construction of genetic linkage maps. It includes several new major features: (i) handling of very large genotyping datasets like the ones generated by GBS; (ii) direct importation and conversion of Variant Call Format (VCF) files; (iii) detection of linkage, i.e. construction of linkage groups in case of segregation distortion; (iv) data imputation on VCF files using a new approach, called LB-Impute. Features i to iv operate through inclusion of new Java modules that are used transparently by MapDisto; (v) QTL detection via a new R/qtl graphical interface.

Availability and implementation

The program is available free of charge at mapdisto.free.fr.

Contact

[e-mail].

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Heffelfinger C 

PROVIDER: S-EPMC5870660 | biostudies-literature | 2017 Jul

REPOSITORIES: biostudies-literature