在基因组学时代，利用 MapDisto 2.0 构建连锁图谱。
Constructing linkage maps in the genomics era with MapDisto 2.0.
机构信息
Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, USA.
DIADE Research Unit, Institut de Recherche pour le Développement (IRD), Montpellier, France.
出版信息
Bioinformatics. 2017 Jul 15;33(14):2224-2225. doi: 10.1093/bioinformatics/btx177.
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
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
动机
测序基因分型 (GBS) 产生的数据集，当前具有图形界面的遗传作图软件难以处理。遗传学家需要新的用户友好型计算机程序，可以在台式计算机上分析 GBS 数据。这需要提高计算效率，包括速度和随机存取存储器 (RAM) 的使用。
结果
MapDisto v.2.0 是一个用于构建遗传连锁图谱的用户友好型计算机程序。它包含几个新的主要功能：(i) 处理大型基因分型数据集，如 GBS 生成的数据集；(ii) 直接导入和转换 Variant Call Format (VCF) 文件；(iii) 检测连锁，即在分离失真的情况下构建连锁群；(iv) 使用称为 LB-Impute 的新方法在 VCF 文件上进行数据插补。功能 i 到 iv 通过包含新的 Java 模块来实现，这些模块由 MapDisto 透明使用；(v) 通过新的 R/qtl 图形界面进行 QTL 检测。
可用性和实现
该程序可在 mapdisto.free.fr 上免费获得。
联系方式
补充信息
补充数据可在 Bioinformatics 在线获得。
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