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Zymo-Research / aladdin-shotgun

MIT License
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Addition of AMR plus plus modules #79

Closed nsharp2 closed 8 months ago

nsharp2 commented 9 months ago

1) Dockerfile updated to contain bwa mem and samtools 2) script to compile sample counts files into one table (amr_long_to_wide.py) and other AMRplusplus scripts added (resistome), SNP verification 3) bwa_align, resistome_run, resistome_results, resistome_snpverify, and resistome_snpresults processes added 4) amrplusplus subworkflow added 4) MEGARes database FASTA and annotations added 5) Resistome class results barchart added to MultiQC report 6) Top 20 mean expression percentage AMR genes added to MultiQC report

zxl124 commented 8 months ago

these changes are covered in a different PR.