The DOI matches its Crossref record; 35 of the 35 references it cites were found in a registry or an index.
HybPiper: Extracting coding sequence and introns for phylogenetics from high‐throughput sequencing reads using target enrichment
Open accessAbstract
Premise of the study: Using sequence data generated via target enrichment for phylogenetics requires reassembly of high‐throughput sequence reads into loci, presenting a number of bioinformatics challenges. We developed HybPiper as a user‐friendly platform for assembly of gene regions, extraction of exon and intron sequences, and identification of paralogous gene copies. We test HybPiper using baits designed to target 333 phylogenetic markers and 125 genes of functional significance in Artocarpus (Moraceae). Methods and Results: HybPiper implements parallel execution of sequence assembly in three phases: read mapping, contig assembly, and target sequence extraction. The pipeline was able to recover nearly complete gene sequences for all genes in 22 species of Artocarpus. HybPiper also recovered more than 500 bp of nontargeted intron sequence in over half of the phylogenetic markers and identified paralogous gene copies in Artocarpus. Conclusions: HybPiper was designed for Linux and Mac OS X and is freely available at https://github.com/mossmatters/HybPiper.
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Cited by
Johnson, M. G., Pokorny, L., Dodsworth, S., Botigué, L. R., Cowan, R. S., Devault, A., Eiserhardt, W. L., Epitawalage, N., Forest, F., Kim, J. T., et al. (2019) · Systematic Biology · doi:10.1093/sysbio/syy086 · Cited by 593
Self-citationPhylogenomics and the rise of the angiosperms
Zuntini, A. R., Carruthers, T., Maurin, O., Bailey, P. C., Leempoel, K., Brewer, G. E., Epitawalage, N., Françoso, E., Gallego-Paramo, B., McGinnie, C., et al. (2024) · Nature · doi:10.1038/s41586-024-07324-0 · Cited by 429
Self-citationSianta, S. A., & Kay, K. M. (2022) · Evolution · doi:10.1111/evo.14484 · Cited by 7
Metadata
- Authors
- Johnson, M. G., Gardner, E. M., Liu, Y., Medina, R., Goffinet, B., Shaw, A. J., Zerega, N. J. C., & Wickett, N. J.
- Venue
- Applications in Plant Sciences
- Publisher
- Wiley
- Published
- 2016-07
- Volume
- 4
- Issue
- 7
- ISSN
- 2168-0450 (ISSN-L)
- OpenAlex
- W2462976181
- Cited by
- 847
- References
- 35
- FWCI
- 9.48
- Type
- journal article
- Language
- en
- Open access
- gold
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- Johnson, M. G., Gardner, E. M., Liu, Y., Medina, R., Goffinet, B., Shaw, A. J., Zerega, N. J. C., & Wickett, N. J. (2016). HybPiper: Extracting coding sequence and introns for phylogenetics from high‐throughput sequencing reads using target enrichment. Applications in Plant Sciences. https://doi.org/10.3732/apps.1600016
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