Transcriptome Assembly Workshop, Spring 2018
National Center for Genome Analysis Support (NCGAS) SPRING WORKSHOP 2018 Schedule
April 30th -May 1st, 2018
The workshop includes discussions, lectures, and hands-on tutorials to cover topics important to getting started constructing and analyzing transcriptomes—without the use of a genome. Material will cover 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.
While material will make heavy use of XSEDE and IU machines, the material is transferable to any cluster.
|9:00am||Introduction to NCGAS and staff||Tom|
|9:30am||Introduction to Clusters and Other Resources||Sheri|
|11:15 am||Optimizing Jobs||Carrie|
|12:15 pm||Data Center Tour|
|2:00pm||Data Management and Movement||Bhavya|
|3:45pm||Introduction to Assembly and Pipeline||Sheri|
|5:00pm||Publicly Available Resources||All|
|10:00 am||Hands on Pipeline Use||All|
|11:30 am||Getting Help in HPC||Sheri/All|
|1:30 pm||Hands on Pipeline Use Cont’d||Sheri/All|
|3:15 pm||DE Analysis||Sheri|
|4:45 pm||Downstream Analyses Discussion||Sheri|
Scripts used in this workshop - Project_Workshop.tar.gz (under releases)
Slides and Presentations - https://iu.box.com/s/3n8fuge8kc92i1snl60jordegk32mrah
NCGAS webpage - https://ncgas.org/WelcomeBasket_Pipeline.php
Scripts in general (SLURM/PBS scripts)- https://github.com/NCGAS/de-novo-transcriptome-assembly-pipeline
Email us at firstname.lastname@example.org