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

Jason R. Miller, Peng Zhou, Joann Mudge, James Gurtowski, Hayan Lee, Thiruvarangan Ramaraj, Brian P. Walenz, Junqi Liu, Robert M. Stupar, Roxanne Denny, Li Song, Namrata Singh, Lyza G. Maron, Susan R. McCouch, W. Richard McCombie, Michael C. Schatz, Peter Tiffin, Nevin D. Young, Kevin A.T. Silverstein

Research output: Contribution to journalArticlepeer-review

45 Scopus citations


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.

Original languageEnglish (US)
Article number541
JournalBMC Genomics
Issue number1
StatePublished - Jul 19 2017

Bibliographical note

Publisher Copyright:
© 2017 The Author(s).


  • Genome assembly
  • Hybrid assembly pipeline
  • Medicago truncatula
  • Tandem repeats


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