A bioinformatics pipeline for analysing short read Illumina data microbiological public health.
Project description
Bohra
A pipeline for analysis of Illumina short reads for public health microbiology.
Motivation
Bohra was inspired by Nullarbor (https://github.com/tseemann/nullarbor) to be used in public health microbiology labs for analysis of short reads from microbiological samples.
Limitations
Bohra is restricted to Illumina read sets. It has been built with the goal of being able to be run in HPC environments, although the configurations at this initial committ have not been included.
Pipeline
Bohra can be run in three modes
- SNPs and Phylogeny
- Clean reads
- Call variants
- Generate a phylogenetic tree
- SNPs, Phylogeny, Typing, Annotation and Species Identification (DEFAULT)
- Clean reads
- Call variants
- Generate a phylogenetic tree
- Assemble
- Species identification
- MLST
- Resistome
- Annotate
- SNPs, Phylogeny, PanGenome and Typing and Species Identification
- Clean reads
- Call variants
- Generate a phylogenetic tree
- Assemble
- Species identification
- MLST
- Resistome
- Annotate
- Pan Genome
Installation
Dependencies
Bohra requires >=python3.6 and is dependent on snakemake
At the moment bohra can only be installed via github - other options will follow
pip3 install snakemake
pip3 install git+https://github.com/MDU-PHL/bohra
If you are installing on a server in your local directory use
pip3 install git+https://github.com/MDU-PHL/bohra --user
Don't forget to add your local installation to your path. For example this should work.
export PATH=~/.local/bin:=$PATH
Initial run
usage: bohra run [-h] [--input_file INPUT_FILE] [--job_id JOB_ID]
[--reference REFERENCE] [--mask MASK]
[--pipeline {sa,s,a,all}]
[--assembler {shovill,skesa,spades}] [--cpus CPUS]
[--minaln MINALN] [--prefillpath PREFILLPATH] [--mdu MDU]
[--workdir WORKDIR] [--resources RESOURCES] [--force]
[--dryrun] [--gubbins]
optional arguments:
-h, --help show this help message and exit
--input_file INPUT_FILE, -i INPUT_FILE
Input file = tab-delimited with 3 columns
<isolatename> <path_to_read1> <path_to_read2>
(default: )
--job_id JOB_ID, -j JOB_ID
Job ID, will be the name of the output directory
(default: )
--reference REFERENCE, -r REFERENCE
Path to reference (.gbk or .fa) (default: )
--mask MASK, -m MASK Path to mask file if used (.bed) (default: False)
--pipeline {sa,s,a,all}, -p {sa,s,a,all}
The pipeline to run. SNPS ('s') will call SNPs and
generate phylogeny, ASSEMBLIES ('a') will generate
assemblies and perform mlst and species identification
using kraken2, SNPs and ASSEMBLIES ('sa' - default)
will perform SNPs and ASSEMBLIES. ALL ('all') will
perform SNPS, ASSEMBLIES and ROARY for pan-genome
analysis (default: sa)
--assembler {shovill,skesa,spades}, -a {shovill,skesa,spades}
Assembler to use. (default: skesa)
--cpus CPUS, -c CPUS Number of CPU cores to run, will define how many rules
are run at a time (default: 36)
--minaln MINALN, -ma MINALN
Minimum percent alignment (default: 0)
--prefillpath PREFILLPATH, -pf PREFILLPATH
Path to existing assemblies - in the form
path_to_somewhere/isolatename/contigs.fa (default:
None)
--mdu MDU If running on MDU data (default: True)
--workdir WORKDIR, -w WORKDIR
Working directory, default is current directory
(default: /home/khhor/dev/bohra)
--resources RESOURCES, -s RESOURCES
Directory where templates are stored (default:
templates)
--force, -f Add if you would like to force a complete restart of
the pipeline. All previous logs will be lost.
(default: False)
--dryrun, -n If you would like to see a dry run of commands to be
executed. (default: False)
--gubbins, -g If you would like to run gubbins. NOT IN USE YET -
PLEASE DO NOT USE (default: False)
Minimal run
bohra run -r path_to_ref -i path_to_input -j job_id
Subsequent run
Once a run has been completed you can rerun bohra
- Add or remove isolates
- Add - add a new tab-delimited line
- Remove - Prepend a
#
to the lines you wish to remove
- Change the reference
- If changing the reference re-alignment and variant calling will be performed
- Change the mask file
usage: bohra rerun [-h] [--reference REFERENCE] [--mask MASK] [--cpus CPUS]
[--workdir WORKDIR] [--resources RESOURCES] [--dryrun]
[--gubbins] [--keep]
optional arguments:
-h, --help show this help message and exit
--reference REFERENCE, -r REFERENCE
Path to reference (.gbk or .fa) (default: )
--mask MASK, -m MASK Path to mask file if used (.bed) (default: )
--cpus CPUS, -c CPUS Number of CPU cores to run, will define how many rules
are run at a time (default: 36)
--workdir WORKDIR, -w WORKDIR
Working directory, default is current directory
(default: /home/khhor/dev/bohra)
--resources RESOURCES, -s RESOURCES
Directory where templates are stored (default:
templates)
--dryrun, -n If you would like to see a dry run of commands to be
executed. (default: False)
--gubbins, -g If you would like to run gubbins. NOT IN USE YET -
PLEASE DO NOT USE (default: False)
--keep, -k Keep report from previous run (default: False)
Rerun with different combination of isolates
bohra rerun
Rerun with different reference/mask
bohra rerun -r pathtonewref -m pathtonewmask
Output
Bohra outputs a directory with a report.html
and all data required for visualisation in a web browser.
Etymology
Bohra is an exinct tree dwelling kangaroo whose fossils have been found in the Nullarbor, before the Nullarbor was treeless. Since this pipeline implements Snippy, named for another famous Australian kangaroo ('Skippy') and designed based on Nullarbor Bohra is an exceedingly appropriate name.
More to follow!!
- Expand readme
- Polish log files
- Add clean functions
Project details
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