snakePipes

snakePipes are pipelines built using snakemake and python for the analysis of epigenomic datasets.
Below is the list of pipelines available in snakePipes
Pipeline |
Description |
---|---|
Create indices for an organism for further use within snakePipes |
|
Basic DNA mapping using bowtie2, filter mapped files, QC and create coverage plots |
|
Use the DNA mapping output and run ChIP/Input normalization and peak calling |
|
Use the DNA mapping output and detect open chromatin regions for ATACseq data |
|
HiC analysis workflow, from mapping to TAD calling |
|
pairtools workflow, from allele-specific mapping to HiC matrices |
|
ncRNAseq workflow : From mapping to differential expression of genes and repeat elements using DESeq2 |
|
RNASeq workflow : From mapping to differential expression using DESeq2 |
|
Single-cell RNA-Seq (CEL-Seq2) workflow : From mapping to differential expression |
|
Whole-genome Bisulfite-Seq analysis workflow, from mapping to DMR calling and differential methylation analysis |
|
Merging technical replicates (e.g., across lanes), removing optical duplicates, running FastQC |
Quick start
Assuming you have python3 with conda, install the latest version of snakePipes with:
conda create -n snakePipes -c mpi-ie -c conda-forge -c bioconda snakePipes
You can update snakePipes to the latest version available on conda with:
conda update -n snakePipes -c mpi-ie -c conda-forge -c bioconda --prune snakePipes
Download genome fasta and annotations for an your organism, and build indexes, Check in createIndices
Configure snakePipes with paths to organism and snakemake configs on your system using snakePipes config. Importantly, take care to set --condaEnvDir parameter, which defaults to /tmp. For detailed information, run:
snakePipes config --help
Note
If you have a copy of a shared/defaults.yaml with the necessary paths configured (i.e. from a previous installation), you can pass it to snakePipes config with --oldConfig and --configMode recycle instead of providing all the paths manually again. Config keys have to match for this to work. In the same way, you can pass your external organism yaml folder with --organismsDir
.
Download example fastq files for the human genome here
Execute the DNAmapping pipeline using the example command.sh in the test data directory.
Running your own analysis
For a detail introduction to setting up snakePipes from scratch, please visit Setting up snakePipes
For each organism of interest, snakePipes requires fasta files, genome indexes and annotation files. Paths to these files are specified in the organism/<name>.yaml files. After installation, the location of these files could be revealed by the following command:
snakePipes info
You could either modify the existing files (add your own paths), or add a new file there. See more detail in Running snakePipes
snakePipes could either be executed locally, or on any snakemake-supported cluster infrastructure. See details for setting up the cluster command in Running snakePipes
Citation
If you adopt/run snakePipes for your analysis, cite it as follows :
Bhardwaj V, Heyne S, Sikora K, Rabbani L, Rauer M, Kilpert F, Richter AS, Ryan DP, Manke T. snakePipes: facilitating flexible, scalable and integrative epigenomic analysis. Bioinformatics. 2019 May 27. pii: btz436. doi:
10.1093/bioinformatics/btz436. [Epub ahead of print] PubMed PMID: 31134269. https://www.ncbi.nlm.nih.gov/pubmed/31134269

This tool suite is developed by the Bioinformatics Unit at the Max Planck Institute for Immunobiology and Epigenetics, Freiburg.
Help and Support
For query/questions regarding snakePipes, please write on biostars with the tag #snakePipes
For feature requests or bug reports, please open an issue on our GitHub Repository.
Contents:
- Setting up snakePipes
- Running snakePipes
- Advanced usage of snakePipes
- Understanding snakePipes implementation
- Calling snakemake directly using the snakefiles
- Executing the Rscript wrappers outside snakePipes
- Updating/adding new tools to the workflows
- Modifying or adding new rules to the workflows
- Using AWS or other cloud platforms
- Receiving emails upon pipeline completion
- createIndices
- DNAmapping
- ChIPseq
- ATACseq
- HiC
- makePairs
- preprocessing
- mRNAseq
- ncRNAseq
- scRNAseq
- WGBS
- snakePipes News