Dataset Information
Hybrid assembly with long and short reads improves discovery of gene family expansions.
Ontology highlight
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 predicted tandemly repeated genes absent from the other assemblies.Conclusion
Our results suggest Alpaca is a useful tool for investigating structural and copy number variation within de novo assemblies of sampled populations.
SUBMITTER: Miller JR
PROVIDER: S-EPMC5518131 | biostudies-literature | 2017 Jul
REPOSITORIES: biostudies-literature
Publications
Hybrid assembly with long and short reads improves discovery of gene family expansions.
BMC genomics 20170719 1
<h4>Background</h4>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.<h4>Methods</h4>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 fo ...[more]
