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Usage overview

Users have the option to supply paired-end fastq (support for ONT coming soon) and/or de novo assemblies as inputs into the pipeline.

  • Paired-end fastq only - where you only have paired-end fastq bohra will generate de novo assemblies if required.

  • de novo assemblies only - where you only have de novo assemblies bohra will not use a reference-based approach for comparative analysis. However, reference-free comparative tools, ska2 and mash are available.

  • Both paired-end fastq and de novo assemblies - in situations where you have de novo assemblies already generate, you can supply both sequence types to bohra. It will use the supplied de novo assemblies for any steps which require them, potentially saving you time.

Additionally, you can also supply the species value and any optional sample metadata that may be useful.

Input file

bohra requires a single tab-delimited file as input, you can find examples [here] TO ADD.

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'. No

Species column

If you do not require speciation as part of the pipeline and already know the species, you can provide it here. Please note if no speciation is undertaken, bohra will use this value to undertake typing and AMR mechanisms/inferrence. If the species in this column is NOT accurate - unexpected results may occur.

Controls

If you include controls in an analysis you can add an is_control column to your input file and supply the type of control. Note that anything designated as a control will have single-sample analyses done (were possible) but will NOT be included in any comparative analyses.

Tree Annotation and additional metadata

You may also provide additional columns of relevant metadata in your input file. bohra will NOT do any data validation on these columns - that is up to the user. But any additional metadata provided will be visible on the tree provided in the report file and the summary table.

bohra can generate the input file for you

If you have

  • A table with a list of isolates and othe data (species or other metadata) (column 'Isolate' must be included)

AND/OR

  • Paths to your reads and/or contigs

bohra can generate the input file for you. 

bohra generate-input --isolate_ids <table_name>.txt --reads /path/to/reads --contigs /path/to/contigs --outname my_data.txt
This will generate a file which you can use as input into bohra.

Note that on large file systems this may take a while

Pipelines

bohra is a flexible pipeline and allows users to customise the workflows used. Below is an overview of each workflow. Links for each workflow can be found below.

Pipelines
basic assembly
amr and typing comparative analysis
full tb

A note on databases

Many bioinformatics tools require the use of a database or data collection. Where possible and appropriate, bohra utilises the databases that come packaged with the tools being used in order to ensure expected behaviour and consistency. However, there are cases were the user will need to supply a database path.

  • kraken2 - these databases are very large and not easily packaged for distribution with software. So the user will either need to have existing databases available or download them as part of the setup of bohra. This information is here

  • mlst comes packaged with a collection of profiles and is ready to use. However, due to changes in licensing, the most up to date profiles cannot be included. As such if you have available to you a current mlst database that is configured for use with mlst you can set the BOHRA_PUBMLST_DB and BOHRA_BLAST_DB environment variables as part of the setup of bohra, as described here