Redmine

07/15/2019

11:37 AM Pathogen outbreak study - Pseudomonas single isolate WGS Check coverage cutoffs for SNP analysis

SNP analysis is done with freebayes (on quality trimmed and filtered reads) with default settings ( -C 2 -min_coverag... Katie Lennard

07/02/2019

02:12 PM Microbiota profiling of cows milk with and without traditional fermentation Data processed with dada2 pipeline on Ilifu

Both read trim strategies and taxonomic DB used will be considered to try and improve species-level resolution compar... Katie Lennard

06/26/2019

01:02 PM Microbiota profiling of cows milk with and without traditional fermentation Meetin with Pieter and Mike to discuss analysis

Mainly they are looking for improved species-level resolution with a few specific species they are hoping to see. I w... Katie Lennard

06/25/2019

05:21 PM The impact of fire and herbivores on soil microbes dada2 testrun on HPC successfull

Config files edited by user (on HPC copy of repo). https://github.com/kviljoen/16S-rDNA-dada2-pipeline/blob/master/co... Katie Lennard