Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
https://github.com/ssi-dk/bps_fbi_scripts_clostyper
Tool to find mge (phages, plasmids, and transposons) in cdiff. Scripts that allow Clostyper to be run in slurm.
https://github.com/ssi-dk/bps_fbi_scripts_clostyper
cdiff clostridioides-difficile clostyper mge phages plasmids transposons
Last synced: 3 days ago
JSON representation
Tool to find mge (phages, plasmids, and transposons) in cdiff. Scripts that allow Clostyper to be run in slurm.
- Host: GitHub
- URL: https://github.com/ssi-dk/bps_fbi_scripts_clostyper
- Owner: ssi-dk
- License: mit
- Created: 2023-07-05T13:50:54.000Z (over 1 year ago)
- Default Branch: master
- Last Pushed: 2023-07-31T09:43:01.000Z (over 1 year ago)
- Last Synced: 2024-04-29T00:16:36.004Z (7 months ago)
- Topics: cdiff, clostridioides-difficile, clostyper, mge, phages, plasmids, transposons
- Language: Python
- Homepage:
- Size: 15.9 MB
- Stars: 0
- Watchers: 4
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# ClosTyper
:warning:__*Please note that clostyper is still in an early stage of development. There may be substantial changes as many features are still being added*__
ClosTyper is a pipeline tool designed to automate characterization and genotyping of selected _Clostrdia_ species using the whole genome sequencing data
ClosTyper is written in Snakemake that allows reproducibility and scalability of the intergrated workflow.
✋ **This tool is under active development** ✋
You may think of use WGSBAC (https://gitlab.com/FLI_Bioinfo/WGSBAC) that combine different generalized modules for bacterial characterization based on WGS data
## Requirements
#### Software requirements
before start, you need to make sure that the follwoing software are installed in your system and that they are available in your $PATH
1. `any2fasta`: Convert various sequence formats to FASTA (https://github.com/tseemann/any2fasta)
- Installation instructions: https://github.com/tseemann/any2fasta#github
- Required version: 0.4.2 ro later
2. `snakemake`: a workflow management system that creates reproducible and scalable data analyses. Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment (https://snakemake.github.io/)
- Installation instructions: https://snakemake.readthedocs.io/en/stable/getting_started/installation.html
- Required version: 6.15.5 or later
3. `pigz`: A parallel implementation of gzip for modern multi-processor, multi-core machines (https://zlib.net/pigz/)
- Installation instructions: https://zlib.net/pigz/
- Required version: 2.3.4 or later
4. `conda`: package, dependency and environment management system (https://docs.conda.io/en/latest/)
- Installation instructions: https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html
#### Databases requirements
1. (Mini)Kraken2 database: taxonomic profiling of sequencing data (https://ccb.jhu.edu/software/kraken2/)
- Download page: https://ccb.jhu.edu/software/kraken2/downloads.shtml
## Installation
#### Install clostyper from source
These instructions will install the latest version of `ClosTyper`:
```
git clone https://gitlab.com/FLI_Bioinfo/clostyper.git
ln -s `pwd`/clostyper/bin/clostyper /usr/local/bin/ # choose a folder in your $PATH
```
This should be the directory structure of clostyper
```
|-- bin
| `-- clostyper
|-- config
| `-- README.md
|-- dbs
| |-- custom_dbs
| `-- trimmomatic.fa
|-- README.md
`-- workflow
|-- envs
|-- rules
|-- scripts
`-- Snakefile
```
## Usage
### First execution
On first execution of clostyper with `clostyper -h`, a config file will be automatically created under the folder .
This file should include the paths to databases and schemes to be used with `clostyper`.
✍ Important: at least the full path to the Kraken2 database must be provided.
## Basic usage [with test data]
#### download test data:
```
wget -O test_data_clostyper.tar.gz https://zenodo.org/record/6656045/files/test_data_clostyper.tar.gz?download=1
tar xzvf test_data_clostyper.tar.gz
```
### Run clostyper
✍ Note: the full path to the Kraken2 database should have been specified in the config file . If not, you must use `--kraken2db `
* **To check raw data quality**
This will only execute the fastp & kraken2
Basic call: `clostyper --check_quality -d [FASTQ_DIRECTORY] -r [REFERENCE] [-o WORKING_DIRECTORY] `
- With the test data
```
clostyper --check_quality -d test_data/input_data/ -r test_data/input_data/ref.gbk -o results_dir -A -T
```
* **To configure and execute the full pipeline**
✍ WARNING: Many features of clostyper are still experimental. Please report issues in the issue tracker (https://gitlab.com/FLI_Bioinfo/clostyper/-/issues)
This will execute the full pipeline
Basic call: `clostyper -d FASTQ/FASTA_DIRECTORY -r REFERENCE [-o WORKING_DIRECTORY] [-s SPECIES]`
- With the test data
```
clostyper -d test_data/input_data/ -r test_data/input_data/ref.gbk -o results_dir -A -T
```
* **To search _C. difficile_ for mobile elements**
To ONLY search your genomes for Clostridium difficile mobile elements, invoke the flag `--run_only_species_wf` together with flag `-s`
- Example with the test dataset
```
clostyper -d test_data/input_data/ -r test_data/input_data/ref.gbk -o results_dir -s cdifficile --run_only_species_wf -A -T
```
### Full usage options
```
> clostyper -h
ClosTyper: Clostridia characterization and typing pipeline
Version: 0.1-beta (available at: https://gitlab.com/FLI_Bioinfo/ClosTyper)
USAGE:
---------------------
clostyper --check_quality -d FASTQ_DIRECTORY [-o WORKING_DIRECTORY]
clostyper -d FASTQ/FASTA_DIRECTORY -r REFERENCE [-o WORKING_DIRECTORY] [-s SPECIES] [--run_cgmlst]
clostyper -t SAMPLE_TABLE -r REFERENCE [-o WORKING_DIRECTORY] [-s SPECIES] [--run_cgmlst]
---------------------
INPUT:
-d, --fastx-directory DIR, a directory where fastq reads or assembled genomes are present. Required unless -t flag was used
Format: [ID]_{1,2}.fastq{.gz} [ID]_S*_R{1,2}_001.fastq{.gz} [ID]_R{1,2}.fastq{.gz} OR [ID].{fasta,fna,fa}
-t, --sample_table FILE (tab delimited), a four-columns based table. See an example in the documentation!
Required unless the -d flag was used. If -t and -d flags were activated, -d will be ignored
-r, --reference FILE, Reference genome. Format: {ID}.{gbk,fasta,gff,embl} (required)
-s, --species Run species-specific workflow (default: False; run only the general workflow)
Currently supported Clostridia species are: cdifficile
OUTPUT:
-o, --output-directory DIR, output directory for the snakemake results (default: output_dir_[timestamp]/)
-w, --overwrite Overwrite an existing directory with the results. Useful to append results to previous runs
-q, --quiet Suppress clostyper messages. Report only warnings, errors and the snakemake call
WORKFLOW:
-Q, --check_quality Quickly perform quality assurance on Illumina data [recommended before doing analysis] [EXPERIMENTAL]
--run_cgmlst Do cgMLST analyis using the chewiesnake pipeline [EXPERIMENTAL]
--run_only_species_wf Execute ONLY the specified species-specific workflow. Require '-s' [EXPERIMENTAL]
--select_reference Select appropriate reference for the SNP anlysis of the dataset [EXPERIMENTAL]
--snp_pipeline Select which pipeline to call SNPs [EXPERIMENTAL]
Supported SNP pipelines are: snippy, reddog, nasp, cfsanpipeline
--kraken2db Path to (Mini)kraken2 DB
--disable_pangenome Disable the pangenome analyis [EXPERIMENTAL]
--disable_report Do not make the html report [EXPERIMENTAL]
OTHERS:
-A, --autorun Automatically run snakemake workflow after configuration (default: False)
-T, --threads Number of threads to use (default: 16)
--check_dep Check if dependencies are ok and then exit
--no-color Do not use a colored output (default: False)
HELP:
-h, --help Show this help and exit
--help_all Show extended help for all software settings options [EXPERIMENTAL]
--version Show clostyper's version number and exit
--citation Show clostyper's citation and exit
```