CircularMapper

A method to improve mappings on circular genomes, using the BWA mapper.

CM is only tested with bwa aln and not with the bwa mem method. You might experience difficulties due to differences how bwa mem handles CIGAR strings in SAM/BAM files and thus are advised to only use bwa aln mapped output.

As this was part of my PhD (> 5yrs ago), I’m not actively maintaining this anymore. If you find bugs, you may open issues but I will not guarantee any bugfixes or even looking at them anymore - code is open source, so if you can and want to fix things, I am however happy to have a look at a PR to fix things.

Author: Alexander Peltzer

Releases

The releases for this project can be found under Releases.

Build the tool manually

We are using Gradle (https://gradle.org/) to build our Java applications, so you’d need to install Gradle (2+) and Java (8+) on your machine to build the executable. Now run:

git clone https://github.com/apeltzer/CircularMapper
cd CircularMapper
gradle build 

After that, you should find the appropriate JAR files in the subdirectories: toolname/build/libs/

A use-case to use this outside of the EAGER pipeline itself, is available here.