pycoSnake is a neatly wrapped collection of snakemake workflows for analysing Illumina and nanopore sequencing datasets. It is easy to install with conda and simple to run on a local computer or in a cluster environment
Conda is the only dependency that you need to install the package.
All the other packages and external program needed for this pipeline will then be automatically handled by conda itself.
Install conda following the official documentation for you system
https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html
You might not need all the extra channels depending on you conda configuration, but you need to add my channel: aleg
conda create -y -n pycoSnake -c aleg -c anaconda -c bioconda -c conda-forge python=3.6 pycosnake
conda activate pycoSnake
To update the package
conda activate pycoSnake
conda update pycoSnake -c aleg
Clone pycoSnake repository to your local machine
git clone git@github.com:a-slide/pycoSnake.git
cd pycoSnake
Create a new conda environment
conda create -y -n pycoSnake python=3.6
conda activate pycoSnake
Install pycoSnake with pip in develop MODE
pip install -e ./
At the moment there is only 2 workflows available in pycoSnake:
-
DNA_ONT : Analyse Basecalled Nanopore sequencing data.
- Download and cleanup genome
- Fastq merging and filtering
- Alignment with minimap2
- Alignment cleaning
- Generate coverage plots IGV and bedgraph (optional)
- Run Nanopore QC with pycoQC (optional)
- Run DNA methylation analysing with Nanopolish + pycoMeth (optional)
- Run SV analysis with Sniffles + filtering + multi-sample merging (optional)
-
RNA_illumina : Analyse Illumina long RNA-seq sequencing data.
- Download and cleanup genome, transcriptome and annotations
- Fastq filtering / control / pre-alignment quality control
- Genome alignment with STAR
- Summarize STAR counts for all samples
- Alignment cleaning
- Transcriptome pseudo-alignment and transcripts quantification with Salmon
- Summarize Salmon counts for all samples
- Generate coverage plots IGV and bedgraph (optional)
- Count reads per genes with featurecounts and summarize counts for all samples (optional)
- Calculation of FPKM with cufflinks and summarize FPKM for all samples (optional)
Generate the sample sheet and config template files required for the workflow you want to run.
conda activate pycoSnake
pycoSnake {WORKFLOW NAME} --generate_template config sample_sheet --overwrite_template
# Or for a cluster environment
pycoSnake {WORKFLOW NAME} --generate_template cluster_config sample_sheet --overwrite_template
The samples.tsv file needs to be filled with the required informations detailed in the file header and passed to pycoSnake (--sample_sheet).
The config.yaml can be modified and passed to pycoSnake (--config). It is generally recommended to stick to the default parameters.
The cluster_config.yaml can be modified and passed to pycoSnake (--cluster_config). Use the file instead of config.yaml if you are executing the pipeline in a cluster environment. By default the file is for an LSF cluster, but it can be modified for other HPC platforms.
Call pycoSnake and choose your workflow
conda activate pycoSnake
pycoSnake {WORKFLOW NAME} {OPTIONS}
Usage on a local machine
conda activate pycoSnake
pycoSnake DNA_ONT -r ref.fa -s sample_sheet.tsv --config config.yaml --cores 10
Usage in an LSF cluster environment
Use the cluster_config option instead of the config file.
The cluster_config provided with pycoSnake is configured to work on an LSF cluster environment
It contains the "prototype bsub command" to be used by Snakemake bsub -q {cluster.queue} -n {cluster.threads} -M {cluster.mem} -J {cluster.name} -oo {cluster.output} -eo {cluster.error} as well as the maximal number of cores and nodes to use.
conda activate pycoSnake
pycoSnake DNA_ONT -r ref.fa -s sample_sheet.tsv --cluster_config cluster_config.yaml
This repository contains snakemake wrappers for pycoSnake.
Wrappers can also be used outside of pycoSnake in any Snakemake file by using the following option:
--wrapper-prefix https://raw.githubusercontent.com/a-slide/pycoSnake/master/pycoSnake/wrappers/
The package contains test data and integrated tests for all the wrappers.
# Test all the wrappers
pycoSnake test_wrappers --cores 8
# Test individual wrappers
pycoSnake test_wrappers --wrappers get_annotation star_count_merge pycometh_comp_report --cores 8
# Keep of test output files generated by the wrappers
pycoSnake test_wrappers --keep_output --cores 8
usage: pycoSnake [-h] [--version] {test_wrappers,DNA_ONT,RNA_illumina} ...
pycoSnake is a neatly wrapped collection of snakemake workflows for analysing
nanopore sequencing data
optional arguments:
-h, --help show this help message and exit
--version show program's version number and exit
subcommands:
pycoSnake implements the following subcommands
{test_wrappers,DNA_ONT,RNA_illumina}
- Development Status :: 3 - Alpha
- Intended Audience :: Science/Research
- Topic :: Scientific/Engineering :: Bio-Informatics
- License :: OSI Approved :: MIT License
- Programming Language :: Python :: 3
Adrien Leger. a-slide/pycoSnake: (2020). doi:10.5281/zenodo.4110611
MIT
Copyright © 2020 Adrien Leger
- Adrien Leger / aleg@ebi.ac.uk / https://adrienleger.com