Abstract Detail

Recent Topics Posters

Cai, Liming [1], Zhang, Hongrui [2], Davis, Charles [3].

PhyloHerb: A high-throughput phylogenomic pipeline for processing genome-skimming data.

Biodiversity research is rapidly accelerated by low-coverage sequencing of total genomic DNA (genome skimming). The genome skimming technique can simultaneously recover the plastid, mitochondrial, and nuclear regions across hundreds of species. PhyloHerb is a command-line-based tool that can efficiently assemble phylogenomic data sets derived from genome skimming. It uses either a built‐in database or user‐specified references to extract orthologous sequences from all three cellular genomes using a BLAST search. It outputs FASTA files and offers a suite of utility functions to assist with alignment, partitioning, concatenation, and phylogeny inference. We also show via simulations that our approach is effective for highly fragmented assemblies from herbarium specimens and is scalable to thousands of species.

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1 - the University of Texas at Austin, Integrative Biology, 205 W 24th St, Austin, Texas, 78712, USA
2 - Harvard University Herbria, 22 Divinity Ave, Cambridge, Massachusetts, 02138, United States
3 - Harvard University, 22 Divinity Avenue, 22 Divinity Avenue, Cambridge, MA, 02138, United States

Keywords:
herbariomics
high-throughput sequencing  .

Presentation Type: Recent Topics Poster
Number: PRT012
Abstract ID:1290
Candidate for Awards:None