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Abstract Detail


Schafran, Peter [1], Li, Fay-Wei [2], Rothfels, Carl [3].

PURC2: an updated pipeline for processing amplicon sequence data from hybrids and polyploids.

The Pipeline for Unraveling Reticulate Complexes (PURC) is a bioinformatics pipeline developed for processing nuclear DNA sequence data from hybrids and polyploids, with a focus on PacBio HiFi (CCS) data. Reads can be demultiplexed by sample and locus, cleaned of chimeric sequences, clustered into each putative source (alleles, homeologs, or paralogs), and alignments output ready for phylogenetic analysis. Here we present an updated version that adds new functionality and allows it to run on 64-bit operating systems. Amplicon sequence variant (ASV) inference via the ‘DADA2’ R package was added as an alternative to OTU clustering, since mock community studies indicate ASV inference often more accurately represents the number of unique sequence sources. On Linux operating systems, the PacBio Long Amplicon Analysis and lima tools replace previous demultiplexing and chimera detection methods. Using sample datasets from Cystopteris and Isoëtes, we demonstrate improved performance in inferring sequences from auto- and allopolyploids.

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1 - Boyce Thompson Institute, 533 Tower Rd., Ithaca, NY, 14853, USA
2 - Boyce Thompson Institute, 533 Tower Rd, Ithaca, NY, 14853, United States
3 - University Of California Berkeley, Berkeley, 94720.0, United States


Presentation Type: Poster
Session: P3, Phylogenomics Posters
Location: Virtual/Virtual
Date: Wednesday, July 21st, 2021
Time: 5:00 PM(EDT)
Number: P3PL027
Abstract ID:1114
Candidate for Awards:None

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