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
Passwordless Authentication and Passwordless Security
It’s no secret — passwords can be a real headache, both for the people who use them and the people who manage them. Over time, we’ve created hundreds of passwords, it’s easy to lose track of them and they’re easily compromised. Fortunately, passwordless authentication is becoming a feasible reality for many businesses. Duo can help you get there.
Rate This Project
Login To Rate This Project
User Reviews
Be the first to post a review of TARGT pipeline!