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