adding HLA-VBseq as a new module
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- Dominant language
- Nextflow
- Stars
- 81
- Forks
- 40
- Avg merge
- 21h 8m
- Merged PRs (30d)
- 1
Description
Description of feature
Algorithm/tool short description
estimate the most probable HLA alleles at full (8-digit) resolution from whole-genome sequence data. HLA-VBSeq simultaneously optimizes read alignments to HLA allele sequences and abundance of reads on HLA alleles by variational Bayesian inference.
Original paper
https://pubmed.ncbi.nlm.nih.gov/25708870/
Source code/binary
http://nagasakilab.csml.org/hla/
Licence
The Licensee agrees to indemnify Tohoku University and hold Tohoku University harmless from and against any and all claims, damages and liabilities asserted by third parties (including claims for negligence) which arise directly or indirectly from the use of the Software or the sale of any products based on the Software.
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by reading the linked original paper and reviewing the HLA-VBSeq source-code or binary reference. Then determine how the requested tool should be represented in this repository and what integration and validation are required; the work is complete when HLA-VBSeq is added as a usable module with its expected behavior verified.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100