Strain-level comparisons across multiple inStrain profiles
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
[ id:'test', single_end:false ]
bams{:bash}
:file
Path to .bam files that were profiled
*.{bam,sam}
profiles{:bash}
:directory
InStrain profile folders
*.IS/
stb_file{:bash}
Path to .stb (scaffold to bin) file that was profiled
*.stb
compare{:bash}
*.IS_compare{:bash}
inStrain compare folders
*.IS_compare/
comparisons_table{:bash}
*.IS_compare/output/*.IS_compare_comparisonsTable.tsv{:bash}
Comparisons table
*.tsv
pooled_snv{:bash}
*.IS_compare/output/*.IS_compare_pooled_SNV_data.tsv{:bash}
Pooled SNV
snv_keys{:bash}
*.IS_compare/output/*.IS_compare_pooled_SNV_data_keys.tsv{:bash}
SNV keys
snv_info{:bash}
*.IS_compare/output/*.IS_compare_pooled_SNV_info.tsv{:bash}
SNV information
versions{:bash}
versions.yml{:bash}
File containing software versions
versions.yml
Calculation of strain-level metrics
