g2gtools creates custom genomes by incorporating SNPs and indels into reference genome, extracts regions of interest, e.g., exons or transcripts, , and converts coordinates of files (bam, gtf, bed) between two genomes. Unlike other liftover tools, g2gtools does not throw away alignments that land on indel regions. Release Version 0.2 can now create personal diploid genomes. The new version still lifts over diploid alignments on personal genome coordinates back to that of reference so we can compare alignments from among samples in a population.
- Free software: MIT License
- Documentation for Release Ver. 1.0.XX: BELOW
- Documentation for Release Ver. 0.2.XX: http://churchill-lab.github.io/g2gtools/.
- Documentation for Release Ver. 0.1.XX: https://g2gtools.readthedocs.org.
- Algorithm design and software engineering: Kwangbom "KB" Choi, Ph. D., The Jackson Laboratory [email protected]
- Software engineering: Matthew J. Vincent, The Jackson Laboratory [email protected]
- Narayanan Raghupathy, The Jackson Laboratory [email protected]
- Anuj Srivastava, The Jackson Laboratory [email protected]
- Mike Lloyd, The Jackson Laboratory [email protected]
A docker file is provided for easy build. We will also be pushing to DockerHub.
The main portion of this release was to upgrade to Python 3.x. Please reach out with any bugs you may encounter.