Tools for dealing with Unique Molecular Identifiers

This repository contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs). Currently there are two tools:

extract: Flexible removal of UMI sequences from fastq reads.

UMIs are removed and appended to the read name. Any other barcode, for example a library barcode, is left on the read.
dedup: Implements a number of different UMI deduplication schemes.

The recommended method is directional_adjecency.

See simulation results at the CGAT blog.

Installation

If you're using Conda, you can use:

conda install -c https://conda.anaconda.org/toms umi_tools

Or pip:

pip install umi_tools

Or if you'd like to work directly from the git repository:

git clone git@github.com:CGATOxford/UMI-tools.git

Enter repository and run:

python setup.py install

To get help on umi_tools run

`umi_tools --help`

To get help on umi_tools extract run

`umi_tools extract --help`

To get help on umi_tools dedup run

`umi_tools dedup --help`

umi_tools is dependent on numpy, pandas, cython, pysam and future