de novo transcriptome assembly workshop - April 30th-May 1st
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Transcriptome Assembly Workshop, Spring 2018

National Center for Genome Analysis Support (NCGAS) SPRING WORKSHOP 2018 Schedule
April 30th -May 1st, 2018
Bloomington, IN


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.

More information here:


Day 1 Activity Lead
8:30 am Registration All
9:00am Introduction to NCGAS and staff Tom
9:30am Introduction to Clusters and Other Resources Sheri
11:00 am BREAK
11:15 am Optimizing Jobs Carrie
12:15 pm Data Center Tour
1:00pm Lunch
2:00pm Data Management and Movement Bhavya
3:30pm BREAK
3:45pm Introduction to Assembly and Pipeline Sheri
5:00pm Publicly Available Resources All
Day 2 Activity Lead
9:00am Using Galaxy Carrie
10:00 am Hands on Pipeline Use All
11:15 am BREAK
11:30 am Getting Help in HPC Sheri/All
12:30 pm Lunch
1:30 pm Hands on Pipeline Use Cont’d Sheri/All
3:00 pm BREAK
3:15 pm DE Analysis Sheri
4:45 pm Downstream Analyses Discussion Sheri

More information

Scripts used in this workshop - Project_Workshop.tar.gz (under releases)
Slides and Presentations -
NCGAS webpage -
Scripts in general (SLURM/PBS scripts)-


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