Accumulate all UMIs and output a tabular file, a BLAST file (fasta) and a zip file.
The tabular file will contain all unique UMI nucleotides, a count of the number of reads that are
associated with that UMI and a read that represents the sequences associated with that umi.
The BLAST file can be used to identify all UMI clusters.
The zip file will contain fasta files for each UMI and the reads associated to it.
Clone this repo in your Galaxy Tools directory:
git clone https://github.com/naturalis/galaxy-tool-UMI-isolation
Make the python script executable:
chmod 755 galaxy-tool-UMI-isolation/getUmiIsolation.sh
chmod 755 galaxy-tool-UMI-isolation/getUmiIsolation.py
Append the file tool_conf.xml:
<tool file="/path/to/Tools/galaxy-tool-UMI-isolation/getUmiIsolation.sh" />
Depending on your setup the ansible.builtin.git module could be used.
Install the tool
by including the following in your dedicated *.yml file:
- repo: https://github.com/naturalis/galaxy-tool-UMI-isolation
file: getUmiIsolation.xml
version: master
This repo is kept as a backup to guarantee continuity for Naturalis.
An author maintained verion of this tool can be found here:
https://github.com/JasperBoom/galaxy-tools-umi-isolation
Active development on this tool is done in the Caltha package:
https://github.com/JasperBoom/caltha
- Giardine B, Riemer C, Hardison RC, Burhans R, Elnitski L, Shah P,
Galaxy: A platform for interactive large-scale genome analysis.
Genome Research. 2005; 15(10) 1451-1455 doi: 10.1101/gr.4086505
GALAXY
- Boom J & Vos RA, galaxy-tool-UMI-isolation. 2019.
Github repository: https://github.com/naturalis/galaxy-tool-UMI-isolation