An optimized approach for local de novo assembly of overlapping paired-end RAD reads from multiple individuals.

ABSTRACT: Restriction site-associated DNA (RAD) sequencing is revolutionizing studies in ecological, evolutionary and conservation genomics. However, the assembly of paired-end RAD reads with random-sheared ends is still challenging, especially for non-model species with high genetic variance. Here, we present an efficient optimized approach with a pipeline software, RADassembler, which makes full use of paired-end RAD reads with random-sheared ends from multiple individuals to assemble RAD contigs. RADassembler integrates the algorithms for choosing the optimal number of mismatches within and across individuals at the clustering stage, and then uses a two-step assembly approach at the assembly stage. RADassembler also uses data reduction and parallelization strategies to promote efficiency. Compare

SUBMITTER: Li YL 

PROVIDER: S-EPMC5830760 | biostudies-literature | 2018 Feb

REPOSITORIES: biostudies-literature