auto build and update microprot_db and HH-suite compatible DB
- Dominant language
- Python
- Stars
- 2
- Forks
- 6
- PR merge metrics
- No merged PRs in 30d
Description
Databases which we build from publicly available and in-house genomic and metagenomic data need to be updatable and we need to generate scripts to automatically generate updates for HH-suite compatible DB.
We need it for the last part of the pipeline `MSA_hhblits` where we search against UniClust30 and (after this issue is resolved) against our `microprot_db`.
Building the seed `microprot_db` is done, now we need to write a script to automatically update current clustering using `mmseqs` and find an effective way to create HH-suite databases from those updated clusterings.
*References:*
MMseqs: https://github.com/soedinglab/mmseqs2/wiki#updating-a-database-clustering-using-mmseqs-clusterupdate
UniClust pipeline (building HHsuite DB): https://github.com/soedinglab/uniclust-pipeline/blob/master/run_hhdatabase.sh
HHsuite (section 4.9): https://github.com/soedinglab/hh-suite/blob/master/hhsuite-userguide.pdf
I've got some preliminary scripts. If interested, please inquire offline.
Contributor guide
No contributing guide indexed for this repository
Research direction
No repository files or tests are identified. Start at the MSA_hhblits pipeline stage, then review the MMseqs clusterupdate reference, UniClust's run_hhdatabase.sh, and HH-suite guide section 4.9. Done means an automated process updates the current microprot_db clustering and produces an HH-suite-compatible database for pipeline searches.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics, data-engineering, databases
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 25/100