jekesa v1.0 - Illumination

New features

• Added bin/06.cgeAMR.sh which makes use of resfinder and Pointfinder tools to detect chromosomal mutations and acquired AMR
• Added salmonella in-depth analysis option to determine serogroups and antigen types
• Now tracking run progress and can resume analysis steps from point of interruption

Minor changes / bugfixes

• Merged scripts for generation of the final MS Excel report
• Detection of AMR variants using ARIBA now based on the ResFinder database
• Results for each analysis step now numbered and included in the final results folder
• Assembled contigs now included in the final results folder in subfolder called assembled-contigs

jekesa v0.2

New features

• Added ConFindr to detect both inter and intra species contamination
• Added virulence factor detection using ARIBA and the VFDB

Minor changes / bugfixes

• Added column for depth of coverage (estimation) in the final excel report

jekesa v0.1

Update README.md