NCGAS national level workshop on de novo transcriptome assembly on Oct 1st to 3rd, 2018
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README.md

Transcriptome Assembly Workshop, Fall 2018

National Center for Genome Analysis Support (NCGAS) SPRING WORKSHOP 2018 Schedule
October 1st and 2nd, 2018
Bloomington, IN

Description

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.

Schedule

Day 1 Activity Lead
8:30 am Registration All
9:00am Introduction to NCGAS and staff Tom
9:45am Introduction to Clusters and Other Resources Sheri
11:15 am BREAK
11:30 am Optimizing Jobs Carrie
12:00 pm Data Center Tour/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 BREAK
10:15 am Using Galaxy (contd) Carrie
11:00 am BREAK
11:15 am Hands on Pipeline Use 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 - 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

Contact

Email us at help@ncgas.org
Website https://ncgas.org/