Workflow for identification of putatively mobile genetic regions from genome assemblies and bed files. callmemobile first runs various prediction tools to classify mobile features of the input genomes and then compiles these results alongside user options and a set of genetic regions to identify which subset of these regions are predicted to be mobile (maybe).
If you use this in your own work, please cite the papers whose tools the workflow uses:
As well as, the paper for which the workflow was written for: [link preprint]
- 1. Introduction
- 2. Dependencies
- 3. Installation
- 4. Usage
- 5. Citation
- 6. Issues
- 7. Changelog
- 8. License
- 9. Contacts
The user provides 2 files in the input/ directory. The first is a file of
files containing each genomic assembly to be analyzed and their respective
paths. This file ends with a .txt. The second is a file of files containing
the bed files of genomic regions to be queried. This file ends with a .beds.
They shoudl share the same basename (i.e. nctc3k.txt and nctc3k.beds) and
should have the same number of lines. Order of the inputs is how we match the
bed file to the genomic assembly, so please ensure they are matched correctly.
- Conda (unless the use of Conda is switched off in the configuration) and ideally also Mamba (>= 0.20.0)
- GNU Make
- Python (>=3.7)
- Snakemake (>=8.0.0)
and can be installed by Conda by
conda install -c conda-forge -c bioconda -c defaults \
make "python>=3.7" "snakemake-minimal>=8.0.0" "mamba>=0.20.0"The rest of the dependencies are installed automatically by Snakemake
when they are requested. The specifications of individual environments
can be found in workflow/envs/,
and they contain:
- bedops
- phigaro
- Biopython
- blast
- cgecore
- csvtk
- seqkit
- plasmidfinder
- MOB-suite
- mobileelementfinder
- pandas
All dependencies across all rules can also be
installed at once by make conda.
Clone and enter the repository by
git clone https://github.com/baymlab/callmemobile
cd callmemobileAlternatively, the repository can also be installed using cURL by
mkdir callmemobile
cd callmemobile
curl -L https://github.com/baymlab/callmemobile/tarball/main \
| tar xvf - --strip-components=1-
Step 1: Provide lists of input files.
For every input, create a txt list of input assemblies in theinput/directory (i.e., asinput/{batch_name}.txt. Use either absolute paths (recommended), or paths relative to the root of the Github repository (not relative to the txt files).Such a list can be generated, for instance, by
findbyfind ~/dir_with_my_genomes -name '*.fa' > input/my_first_batch.txt
The supported input files should be in FASTA format.
Next, create another txt list of input beds in the
input/directory.find ~/dir_with_my_beds -name '*.bed' > input/my_first_batch.beds
These should follow the format of typical bed files:
➜ head NCTC10036-assembly_abr-search.abr.bed ENA|LR134493|LR134493.1_388 406996 410142 adeF ENA|LR134493|LR134493.1_694 718039 718224 rsmA ENA|LR134493|LR134493.1_1759 1957864 1958496 CRP
The first column corresponds to the contig, the second column is the position start coordinate and the third column is the end coordinate. The fourth column can be any string description of the region (in this case, the gene name).
-
Step 2 (optional): Adjust configuration.
By editingconfig.yamlit is possible to specify parameters of the run, both in terms of options for individual tools and the heuristics employed to deem a region as potentially mobile. -
Step 3: Run the pipeline.
Run the pipeline by runningmake all; this is run Snakemake with the corresponding parameters. -
Step 4: Retrieve the output files.
All output files will be located inoutput/.
The workflow can be configured via the config.yaml file, and
all options are documented directly there. The configurable functionality includes:
- prophage_maxdist: base pair distance from a predicted prophage to classify it as potentially mobile
- integron_pctolap: percent overlap of given region with an integron to classify it as potentially mobile
- mobileelement_maxdist: distance between two mobile elements of the same type to classify it as potentially mobile
- plasmidfinder_mincov: minimum coverage for plasmidfinder to classify a contig as a possible plasmid
- plasmidfinder_threshold: minimum threshold for plasmidfinder to classify a contig as a possible plasmid
callmemobile is executed via GNU Make, which handles all parameters and passes them to Snakemake.
Here's a list of all implemented commands (to be executed as make {command}):
######################
## General commands ##
######################
all Run everything (the default subcommand)
help Print help messages
conda Create the conda environments
clean Clean all output archives and files with statistics
cleanall Clean everything but Conda, Snakemake, and input files
cleanallall Clean completely everything
###############
## Reporting ##
###############
viewconf View configuration without comments
reports Create html report
####################
## For developers ##
####################
test Run the workflow on test data (P1)
bigtest Run the workflow on test data (P1, P2, P3)
format Reformat all source code
checkformat Check source code formatNote: make format and make checkformat require
YAPF and
Snakefmt, which can be installed by
conda install -c conda-forge -bioconda yapf snakefmt.
Tests can be run by make test.
[todo]
todoPlease use Github issues.
See Releases.