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.

ℹ️ 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

The releases for this project can be found under Releases.

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.