Abstract Detail

Conference Wide

Jin, JianJun [1].

Disentanglement of rings: a practical introduction to assembling plastomes and mitogenomes from NGS and LRS data.

Organelle DNA markers and genome sequences are easily obtained and have been extensively used for systematics and DNA barcoding by botanists, taxonomists, ecologists, and geneticists. Due to the high copy numbers of organelle genome in a single cell, it is feasible to get enough reads from the low coverage whole genome sequencing (WGS) data to assemble complete organelle genomes. We developed GetOrganelle, a fast and versatile toolkit for accurate de novo assembly of organelle genomes. According to several benchmark tests of ours and others, GetOrganelle significantly outperforms other available organelle genome assemblers (previously mainly plastome-focused) in completeness, consistency and accuracy. In this hands-on workshop, I will first provide an overview of GetOrganelle toolkit and its applications, and then demonstrate assembling plastomes and mitogenomes from WGS dataset, as well as meta-genomic datasets. Participants will be able to process supplied datasets or their own datasets (plastome or fungal mitogenome preferred in a limited time). I will further interpret the results, and demonstrate a few downstream analysis such as isomer verification and marker recruitment.

1 - Columbia University, Ecology, Evolution And Environmental Biology, 1200 Amsterdam Ave, New York, NY, 10025

none specified

Presentation Type: Workshop
Number: W02001
Abstract ID:19
Candidate for Awards:None

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