Identification and quantification of chimeric sequencing reads in a highly multiplexed RAD-seq protocol.

ABSTRACT: Highly multiplexed approaches have become common in genomic studies. They have improved the cost-effectiveness of genotyping hundreds of individuals using combinatorially barcoded adapters. These strategies, however, can potentially misassigned reads to incorrect samples. Here, we used a modified quaddRAD protocol to analyse the occurrence of index hopping and PCR chimeras in a series of experiments with up to 100 multiplexed samples per sequencing lane (639 samples in total). We created two types of sequencing libraries: four libraries of type A, where PCRs were run on individual samples before multiplexing, and three libraries of type B, where PCRs were run on pooled samples. We used fixed pairs of inner barcodes to identify chimeric reads. Type B libraries show a higher percentage of mi

SUBMITTER: Martin Cerezo ML 

PROVIDER: S-EPMC9796921 | biostudies-literature | 2022 Nov

REPOSITORIES: biostudies-literature