v0.11.1

• Parse AdapterTriming.txt file to get the exact number of bases trimmed
• Add blast based contamination check
• Calculate and upload evenness of coverage for samples
• Change the duplicate marking tool to biobambam2
• Add ability to stop cleanly any analysis driver process with --stop
• Updated EGCG-Core to v0.6

v0.11

• Using our own fastq filterer after bcl2fastq instead of Sickle
• Added a genome size calculation
• quiet=True has been added to Rest API calls in dataset, so it should no longer spam the logs in debug mode
• Basic Lims information is now being gathered and pushed to the reporting app early in the pipeline
• Updated EGCG-Core to v0.5.
• Various refactors in contamination_checks, dataset, dataset_scanner, report_crawlers

v0.10.1

This minor release add:

• ti/tv and het/hom ration calculation
• bases coverage at 5, 15 and 30X + percentile

v0.11

• Using our own fastq filterer after bcl2fastq instead of Sickle
• Added a genome size calculation
• quiet=True has been added to Rest API calls in dataset, so it should no longer spam the logs in debug mode
• Basic Lims information is now being gathered and pushed to the reporting app early in the pipeline
• Updated EGCG-Core to v0.5.
• Various refactors in contamination_checks, dataset, dataset_scanner, report_crawlers