Download
The 'TARGT' pipeline for Targeted Analysis of sequencing Reads for GenoTyping can be used for genotyping of MHC/HLA genes (or other genomic regions) from ancient and modern shotgun sequence data with moderate to low sequence coverage. The pipeline consists of a main bash script that calls the different steps of the pipeline and can either be called directly or submitted to a cluster queue system, as well as additional sub-scripts and files, that are required to perform the different steps. The pipeline also requires installed versions of the mapping tool Bowtie2 and samtools.
Features
- Genotyping of HLA genes from low-coverage sequence data
- HLA allele calling from ancient DNA
- Works for both ancient and modern DNA data
- Can be adapted to other target regions easily
Other Useful Business Software
Try Google Cloud Risk-Free With $300 in Credit
Use your credit across every product. Compute, storage, AI, analytics. When it runs out, 20+ products stay free. You only pay when you choose to.
Rate This Project
Login To Rate This Project
User Reviews
Be the first to post a review of TARGT pipeline!
