Make Pear run optionally
Add SPAdes 3.10.1
Save reports in json (optional)
Get maximum reads length from fastQintegrity for downstream modules
indenpendency
Save excluded contigs (optional)
Save assembly mapping coverage before and after filtration
Assembly mapping Qa/QC based on coverage after filtration
Gene presence/abscence in trueCoverage relies also in gene identity
In trueCoverage remove bases with Phred score lower than 7
Add Yersinia enterocolitica trueCoverage files set and Streptococcus
agalactiae trueCoverage files set (the latter based on MLST genes)
Change subprocess timeout kill
Change programs version check
Update README
Make Pear run optionally Add SPAdes 3.10.1 Save reports in json (optional) Get maximum reads length from fastQintegrity for downstream modules indenpendency Save excluded contigs (optional) Save assembly mapping coverage before and after filtration Assembly mapping Qa/QC based on coverage after filtration Gene presence/abscence in trueCoverage relies also in gene identity In trueCoverage remove bases with Phred score lower than 7 Add Yersinia enterocolitica trueCoverage files set and Streptococcus agalactiae trueCoverage files set (the latter based on MLST genes) Change subprocess timeout kill Change programs version check Update README