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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.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-017-3927-8) contains supplementary material, which is available to authorized users.

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