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Andermann, Tobias [1].

Processing raw Illumina DNA data into alignments for phylogenetic analyses.

During this hands-on data processing workshop we will be  using the  SECAPR  pipeline ( to process Illumina data produced by target capture enrichment (or any other Illumina data) into multiple sequence alignments. Many researchers are producing large Illumina DNA datasets which can be very challenging to process and analyze, particularly when lacking an extensive bioinformatic background, and especially when working with plant DNA data, which often harbour additional complications such as paralogy and polyploidy. SECAPR is a user-friendly pipeline that makes processing of raw Illlumina data into multiple sequence alignments for phylogenetic analyses very simple and straightforward, and which explicitely deals with issues such as paralogy. It also includes a mechanism to phase Illumina short reads into separate alleles at each locus and process these into full sequences that can be utilized in phylogenetics and population genetics. During the workshop we will work on a small and manageable toy example Illumina dataset. The workshop will include installation of the SECAPR pipeline, processing raw Illumina reads into multiple sequence alignments, and phylogenetically analyzing these alignments.

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1 - University of Gothenburg, Biological and Environmental Sciences

none specified

Presentation Type: Workshop
Session: W17, Processing raw Illumina DNA data into alignments for phylogenetic analyses
Location: Virtual/Virtual
Date: Sunday, July 18th, 2021
Time: 1:00 PM(EDT)
Number: W17001
Abstract ID:1111
Candidate for Awards:None

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