This repository contains a number of tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs). Currently there are two tools:
- extract_umi.py: 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_umi.py: Implements a number of different UMI deduplication schemes.
The recommended methods are directional_adjecency and adjecency. In general directional_adjecency seems to be less sensitive to starting conditions, but there are situations where adjecency might out perform.
See simulation results at the CGAT blog.
Both tools are just python scripts. Type
` python dedup_umi.py --help`
or
` python extract_umi.py --help`
for help. dedup_umi.py is dependent on numpy, pandas and both are dependent, at the moment, on CGAT.