Developing best practices for genotyping-by-sequencing analysis in the construction of linkage maps.

ABSTRACT:

Background

Genotyping-by-sequencing (GBS) provides affordable methods for genotyping hundreds of individuals using millions of markers. However, this challenges bioinformatic procedures that must overcome possible artifacts such as the bias generated by polymerase chain reaction duplicates and sequencing errors. Genotyping errors lead to data that deviate from what is expected from regular meiosis. This, in turn, leads to difficulties in grouping and ordering markers, resulting in inflated and incorrect linkage maps. Therefore, genotyping errors can be easily detected by linkage map quality evaluations.

Results

We developed and used the Reads2Map workflow to build linkage maps with simulated and empirical GBS data of diploid outcrossing populations. The workflows run GATK, S

SUBMITTER: Taniguti CH 

PROVIDER: S-EPMC10603770 | biostudies-literature | 2022 Dec

REPOSITORIES: biostudies-literature