MultiplexSSR: A pipeline for developing multiplex SSR-PCR assays from resequencing data.

ABSTRACT: Next-generation sequencing has greatly promoted the investigation of single nucleotide polymorphisms, while studies of simple sequence repeats are sharply decreasing. However, simple sequence repeats still present some advantages in conservation genetics. In this study, an end-to-end pipeline referred to as MultiplexSSR was established to develop multiplex PCR assays in batches with highly polymorphic simple sequence repeats for capillary platforms from resequencing data. The distribution of single sequence repeats in the genome, the error profiles of genotypes and allelotypes, and the increase in the allele length range depending on the number of individuals were investigated. A total of 98% of single sequence repeats presented lengths of less than 100 bp. The error rate of the genotyping

SUBMITTER: Guo L 

PROVIDER: S-EPMC7083706 | biostudies-literature | 2020 Mar

REPOSITORIES: biostudies-literature