Inputs
Input file
bohra requires a tab-delimited file detailed below.
| Column name | Description | Required? |
|---|---|---|
| Isolate | This is the name of the sequence or sample and will appear throughout bohra outputs. It must be unique. |
Yes |
| r1 | The path to read 1 | If an assembly file is not supplied you must supply reads |
| r2 | The path to read 2 | If an assembly file is not supplied you must supply reads |
| assembly | The path to the assembly for the isolate | If reads are not supplied you must supply an assembly file |
| Species_expected | The expected species of the sample or 'control'. the proper species name (not the _ joined name from amrfinder) | No |
bohra can generate the input file for you
If you have
-
Paths to your reads and/or contigs
-
(Optional) A table with a list of isolates and other data (species or other metadata) (column 'Isolate' must be included)
bohra can generate the input file for you.
Reference file
If you are running bohra using one of the comparative pipelines with snippy as the comparative tool, then you will need to supply a reference file. bohra can accept any format, .fa*, .gbk and gz files. File format will be converted to .fasta for use with snippy.