Code to analyse long read mappings, specifically tailored for Oxford Nanopore Reads.

Requirements

• git
• python 2.7
• pysam

I'm pondering using virtualenv to eliminate the pysam dependency and allow other packages to be installed, but then you need to have virtualenv installed.

Installation

To install the code run:

git clone git://github.com/mitenjain/nanopore.git
cd nanopore
git pull
git submodule update --init
make

Testing

To test the installation run:

make test

This will run the demo sequences across the analyses in the test/ directory. The test sets mirrors the process of analysing your own data (see Analysing your own data).

Updating the installation

To update a progressiveCactus installation, from the nanopore base directory type:

git pull
git submodule update --init
make clean
make

Analysing your own data

The inputs are: (1) One or more read files, in FASTA format. These should be placed in the directory nanopore/readFastaFiles. (2) One or more reference genomes, in FASTA format. These should be placed in the directory nanopore/referenceFastaFiles.

For each possible pair of read file, reference genome and mapping algorithm an experiment directory will be created in the nanopore/output directory.

To run the pipeline from the nanopore base directory type:

make run

To clean up an old run type:

make clean

To see and control which mappers and analyses are being run edit lines 8 and 9 of the src/pipeline.py script.