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Supercomputing for Everyone Series: de novo Assembly of Transcriptomes Using HPC Resources

Presenters: Thomas Doak, Carrie Ganote, Bhavya Papudeshi, Sheri Sanders
Organizer: Robert Ping
When:
10/01/2018 and 10/02/2018, 8am-5:30pm

Where: Indiana University, Bloomington, Indiana, 47408


NOTE: This workshop takes place over 2 days. Attendees must attend BOTH days.

The National Center for Genome Analysis Support (NCGAS) offers this two-day workshop on HPC usage and de novo transcriptome assembly.  The workshop consists of discussions, lectures, and hands-on tutorials, to cover topics important to getting started constructing and analyzing transcriptomes—without the use of a genome.  Material covers both the availability and use of high performance computing (HPC) resources, alongside the task of assembling a new transcriptome, in order to provide a more comprehensive preparation for this and future bioinformatic tasks.  Transcriptome assembly will consist of using four separate assemblers (Trinity, SOAP de novo, Velvet Oases, and TransABySS), with multiple kmers, to be combined and curated with Evigenes.  This combined assembly with multiple parameters is considered much more robust than simply using one assembler, and the NCGAS pipeline streamlines the process and allows for customization if desired. We will also discuss downstream analyses such as differential expression and annotation. While material will make heavy use of XSEDE and IU machines, the material is transferable to any cluster.

Participation in this two-day workshop is by invitation only - but you must register to be considered.  Participation is limited by the facilities to 25 people.

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