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  • 65-mock-identify-characterize-genes-in-flye-which-explain-low-q-s-ration-in-diamond-hits
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Created with Raphaël 2.2.07Oct29Sep221615141110928Aug212019181716141310331Jul302423222017161413109872130Jun2926252414131211109843230May2928272615141312119876130Apr29262524232221201918161525Mar191817envs: simplified yaml for bbmap/fastqc/nanostatnew conda YAML for flye (issue #90)updated GDB config files (issue #54)host contamination filtering w/ bbmap/bbtools (issue #54); other minor changesadded comment to diamond rulenotes: script for segmentation analysis of contig cov (issue #84)report: updated plots (mostly themes)notes: plots and multimodality test for contig cov (issye #84)report: added shapes to cdhit scatter plotreport: changed zoom in gene length plotreport: updated cdhit plots (issue #84)report: minor change in report.R (axis titles in gene len fig)report: new cdhit summary and plots (issue #84); other minor changesreport: rm pack version from r.yaml (prev env version cannot be recreated)mapping/coverage: added utils/rule for ave gene/protein cov (issue #84)mapping: changed genomecove_bg to per base coverage (issue #84)mapping: minor change in targets (ave cov for filtered contigs); new rule/targets (issue #84)issue #77: cov plot example - updatedissue #77: cov plot exampleMerge branch 'master' of ssh://git-r3lab-server.uni.lu:8022/susheel.busi/ont_pilot_gitlabissue #77: notes to collected and plot stats for specialtigs (cdhit results)Update Snakefilereport: minor updates for the plotsreport: fixed a bug in rule collecting cdhit resultsupdated readme; configs: updated conda env path in all sbatch.sh filesreport: updated names/colors of assemblers in utils.Rconfigs: sbatch.sh: run snakemake only if conda env activation has workednotes: updated mashmap scriptUpdate sbatch.shZymo/GSI20 configs: replaced main conda env pathreadme updatenotes: mashmap updateGIS20/Zymo configs: fixed a typonotes: mashmap (issue #35)updated configspolishing update: changed polishing strategy, updated racon conda yaml to replace bwa conda yaml (issue #81)notes: diamond test (issue #78)notes: infernal testreport: numbers of cdhit stats (table)better expression to list targets for assembly step