Transcriptome Assembly Workshop, Fall 2018
National Center for Genome Analysis Support (NCGAS) SPRING WORKSHOP 2018 Schedule
October 1st and 2nd, 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.
Updates from last workshop- This workshop we have also included transcriptome annotation of the assembled transcripts using Trinotate, which uses mutiple well referenced annotation tools- BLAST, HMMER, PFAM, RNAMMER, etc and combines all these outputs to one table.
While material will make heavy use of IU machines, the material is transferable to any cluster.
|9:00am||Introduction to NCGAS and staff||Tom|
|9:45am||Introduction to Clusters and Other Resources||Sheri|
|11:30 am||Optimizing Jobs||Carrie|
|12:00 pm||Data Center Tour/Lunch|
|2:00pm||Data Management and Movement||Bhavya|
|3:45pm||Introduction to Assembly and Pipeline||Sheri|
|5:00pm||Publicly Available Resources||All|
|10:15 am||Using Galaxy (contd)||Carrie|
|11:15 am||Hands on Pipeline Use||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/3xo07ugnl7d3q2p2hy4qy0ow1n7blhtn
NCGAS webpage - https://ncgas.org/WelcomeBasket_Pipeline.php
HPC keywords - At the end of the workshop, I moved the HPC keywords to the boxlink and the github repository