Activity
From 04/17/2018 to 05/16/2018
05/16/2018
- 02:41 PM Support #50: Validate binning using single copy core genes
- checkM successfully run on hex. Example outputs listed under the 'Files' tab (checkm.e1851691.txt and checkm.o1851691...
- checkM run report (see Issues)
- Bin QC report generated using checkM (see Issues)
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...
05/07/2018
- See Wiki for details - pipeline development scripts
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...
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...
- 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... - 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 ...
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...
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... - Paper sent by Ulas: their study to demonstrate pipeline we'll be using
- Paper sent by Ulas: a study that used the pipeline we'll be using
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