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Supercomputing for Everyone Series: de novo assembly of transcriptomes using HPC resources workshop

Integrative Data Science Initiative

Start

February 25, 2019
7:00 PM

End

March 1, 2019
7:00 PM

Indiana University, Bloomington, Indiana, 47408

Description

Supercomputing for Everyone Series: de novo assembly of transcriptomes using HPC resources workshop

APPLICATION DEADLINE FRIDAY MARCH 1st at 5pm!

The National Center for Genome Analysis Support (NCGAS) at Indiana University seeks interested participants for this FREE National Science Foundation-sponsored three-day workshop.

Registration page: http://go.iu.edu/29rf 

Registration is FREE, deadline to register is February 25th.

NCGAS is offering a National Science Foundation-sponsored, three-day workshop on high performance computing (HPC) usage and de novo transcriptome assembly. It will take place April 29-May 1st on the IU Bloomington campus. Registration is free, but application is required. Generally we have been teaching this workshop twice a yesr, but this year we will only be teaching it in the Spring. 

The workshop will include 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 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.

While material will make heavy use of XSEDE and IU machines, the material is transferable to any cluster.

Contact Details

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Purdue University, West Lafayette, IN 47907 (765) 494-4600

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