Setting up a portable metagenome assembly pipeline for CBIO

04/26/2018

04:39 PM Support #45 (New): Quality trimming with Trimmomatic

In short after a bit of a struggle to optimize parameters for quality trimming with Trimmomatic I recommend rather us... Katie Lennard

01:13 PM Support #27: What we already know and have setup

Hi Katie,
Regarding metabat.
1. Yes it is dockerised but Hex does not support that so we would need to convert... Gerrit Botha

09:51 AM Support #27: What we already know and have setup

Thanks Gerrit,
This workflow https://bitbucket.org/berkeleylab/metabat is also an option - it is dockerised, uses ... Katie Lennard

04/25/2018

03:24 PM Support #27: What we already know and have setup

I met the developer of this workflow: https://github.com/alesssia/YAMP at the Nextflow workshop last year. I do not t... Gerrit Botha

04/20/2018

03:35 PM Support #38 (New): How to download SRA files to hex

How to download input files (testdata) from SRA to hex:
Use sra-tools installed on hex (activate by doing ‘load modu... Katie Lennard

02:19 PM ismej201625a.pdf

Paper sent by Ulas: their study to demonstrate pipeline we'll be using Katie Lennard

02:18 PM Genome Res.-2013-Sharon-111-20.pdf

Paper sent by Ulas: a study that used the pipeline we'll be using Katie Lennard

04/11/2018

02:26 PM Support #27: What we already know and have setup

Ok Gerrit Botha

02:25 PM Support #27: What we already know and have setup

No problem Gerrit. No, Jai only got as far as asking Andrew to install the necessary software.
Katie Lennard

02:22 PM Support #27: What we already know and have setup

Hi Katie,
I picked up this message from you on the bst-redmine@cbio.uct.ac.za account.
*"Gerrit this was wit... Gerrit Botha