Setting up a portable metagenome assembly pipeline for CBIO

05/11/2018

11:37 AM Support #50 (New): Validate binning using single copy core genes

The quality of the binning results from CONCOCT can be examined by looking at single copy core genes (i.e. genes that... Katie Lennard

04/30/2018

11:42 AM Bug #46 (New): Read binning with CONCOCT

CONCOCT “bins” metagenomic contigs. Metagenomic binning is the process of clustering sequences into clusters correspo... Katie Lennard

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