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

• 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.

To install the code run:

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

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).

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

git pull
git submodule update --init
make clean
make

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.