HLA
xHLA: Fast and accurate HLA typing from short read sequence data (by humanlongevity)
octopus
Bayesian haplotype-based mutation calling (by luntergroup)
| HLA | octopus | |
|---|---|---|
| 2 | 1 | |
| 96 | 298 | |
| - | 0.7% | |
| 0.0 | 4.0 | |
| 8 months ago | 10 months ago | |
| Jupyter Notebook | C++ | |
| GNU General Public License v3.0 or later | MIT License |
The number of mentions indicates the total number of mentions that we've tracked plus the number of user suggested alternatives.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
HLA
Posts with mentions or reviews of HLA.
We have used some of these posts to build our list of alternatives
and similar projects.
-
HLA-Genotyping
xHLA on GitHub worked for me running it directly on the Nebula cram file with no additional processing. Results match those from OptiType (which had high memory requirements, was much slower and only covered 3 of the 6 common genes).
-
HLA Typing from Nebula NGS Data
In the meantime, when I looked over the list again I noticed a docker download for humanlongevity/HLA. I've had some success but the output is only HLA A, B, C, DPB1, DQB1, and DRB1. I'm not sure if I can update some of the resources to get it to do others I am interested in or if I will try something else.
octopus
Posts with mentions or reviews of octopus.
We have used some of these posts to build our list of alternatives
and similar projects.
-
genotyping tool
Check out octopus https://github.com/luntergroup/octopus
What are some alternatives?
When comparing HLA and octopus you can also consider the following projects:
megahit - Ultra-fast and memory-efficient (meta-)genome assembler
TileDB-VCF - Efficient variant-call data storage and retrieval library using the TileDB storage library.
rare-disease-wf - (WIP) best-practices workflow for rare disease