Hybrid assembly with long and short reads improves discovery of gene family expansions.

ABSTRACT:

Background

Long-read and short-read sequencing technologies offer competing advantages for eukaryotic genome sequencing projects. Combinations of both may be appropriate for surveys of within-species genomic variation.

Methods

We developed a hybrid assembly pipeline called "Alpaca" that can operate on 20X long-read coverage plus about 50X short-insert and 50X long-insert short-read coverage. To preclude collapse of tandem repeats, Alpaca relies on base-call-corrected long reads for contig formation.

Results

Compared to two other assembly protocols, Alpaca demonstrated the most reference agreement and repeat capture on the rice genome. On three accessions of the model legume Medicago truncatula, Alpaca generated the most agreement to a conspecific reference and predict

SUBMITTER: Miller JR 

PROVIDER: S-EPMC5518131 | biostudies-literature | 2017 Jul

REPOSITORIES: biostudies-literature