exfi_validation: A Snakemake workflow to validate exfi's performance

1. Description

Workflow to:

• Find putative exons (exfi, biobloomtools, abyss-bloom, bedtools)
• Map agaist different exonic, transcriptomic and genomic references (bwa + samtools)
• Check precision/recall values (bedtools)
• Make reports

2. First steps

Follow the contents of the .travis.yml file:

0. Install (ana|mini)conda

• Anaconda

• miniconda

1. Clone this repo and install

   git clone --recursive https://github.com/jlanga/exfi_validation.git
   cd exfi_validation/
   bash bin/install/from_src.sh

2. Execute the pipeline:

   snakemake --use-conda -j

Once you know it works, edit the config.yaml with paths to your data

3. File organization

The hierarchy of the folder is the one described in A Quick Guide to Organizing Computational Biology Projects:

smsk
├── bin: your binaries, scripts, installation and virtualenv related files.
├── data: raw data, hopefully links to backup data.
├── README.md
├── results: processed data.
|   ├── raw: links to raw data. For your security.
|   ├── exfi: products from the exfi pipeline: bloom filter, gfa with the splice graph, exons.fa with just the exons
|   ├── pr: precision/recall values
|   └── bwa: exons vs reference and some stats.
└── src: additional source code: snakefiles, env files, submodules to other repos.

Bibliography

• A Quick Guide to Organizing Computational Biology Projects

• Snakemake—a scalable bioinformatics workflow engine