styczynski / bioseqdb

# BioseqDB
BioseqDB is a PostgreSQL extension for storing, indexing and searching biological sequences with SQL. Combine genomic matches with relational data using compact sequence types and columnar storage!
Experimental, unsigned alpha packages are provided for ARM64 and x86-64 Linux distributions and MacOS on SourceForge here.
The docker images depend on the Linux distribution and Postgres major version, so please check which PG version you want.
## Table of contents
- Docker quick start
- Packages and Docker images
- SQL walkthrough
 - Alpha-version limitations
 - 1. Create a sequence table
 - 2. Insert patient data
 - 3. Read metadata (non-seqence) columns
 - 4. Reading sequences
 - 5. Read plan for metadata query
 - 6. Alignmment query
 - 7. Trigger index rebuild
 - 8. Repeated search
 - 9. Change algorithms for one call
 - 10. Explaining the search (lots of fields!)
 - 11. Self-alignment query
 - 12. Compare rows using a self-join
 - 13. Load a FASTA file into another table
 - 14. Slices
 - 15. Every possible alignment field
 - 16. Aggregate metadata
 - 17. Explain now the query
 - 18. Update/insert and index rebuild
 - 19. Index statistics
 - 20. Try scalar minimizers, scalar chaining and KSW2
 - 21. Combine sequence operations and an edit filter
- Automatic index updates
## Docker quick start
Ubuntu 26.04 + PostgreSQL 19 (prerelease), for amd64 or arm64. Pull the image:
 [code] 
Now run the container:
 [code] 
Wait for startup:
 [code] 
Now execute client inside the container:
 [code] 
At the psql prompt:
 [code] 
## Packages and Docker images
Release `0.1.0-alpha.1`. Linux package filenames use `4.2.3`.
Choose the matching distribution and PostgreSQL major.
| Distribution | PostgreSQL | Docker (x86-64 and ARM64) | x86-64 binary | ARM64 binary |
|---|---|---|---|---|
| Ubuntu 26.04 | 17 | 0.1.0-alpha.1-pg17-ubuntu26.04 | x86-64 | ARM64 |
| Ubuntu 26.04 | 18 | 0.1.0-alpha.1-pg18-ubuntu26.04 | x86-64 | ARM64 |
| Ubuntu 26.04 | 19 (prerelease) | 0.1.0-alpha.1-pg19-ubuntu26.04 | x86-64 | ARM64 |
| Ubuntu 26.04 | 20 (development) | 0.1.0-alpha.1-pg20-ubuntu26.04 | x86-64 | ARM64 |
| Debian 13 | 17 | 0.1.0-alpha.1-pg17-debian13 | x86-64 | ARM64 |
| Debian 13 | 18 | 0.1.0-alpha.1-pg18-debian13 | x86-64 | ARM64 |
| Debian 13 | 19 (prerelease) | 0.1.0-alpha.1-pg19-debian13 | x86-64 | ARM64 |
| Debian 13 | 20 (development) | 0.1.0-alpha.1-pg20-debian13 | x86-64 | ARM64 |
| Arch Linux | 17 | 0.1.0-alpha.1-pg17-arch | x86-64 | ARM64 |
| Arch Linux | 18 | 0.1.0-alpha.1-pg18-arch | x86-64 | ARM64 |
| Arch Linux | 19 (prerelease) | 0.1.0-alpha.1-pg19-arch | x86-64 | ARM64 |
| Arch Linux | 20 (development) | 0.1.0-alpha.1-pg20-arch | x86-64 | ARM64 |
| Fedora 44 | 17 | Not published | x86-64 | ARM64 |
| Fedora 44 | 18 | Not published | x86-64 | ARM64 |
| Fedora 44 | 19 (prerelease) | Not published | x86-64 | ARM64 |
| Fedora 44 | 20 (development) | Not published | x86-64 | ARM64 |
| openSUSE 16.0 | 17 | Not published | x86-64 | ARM64 |
| openSUSE 16.0 |