Releases: LeeBergstrand/BackBLAST_Reciprocal_BLAST
First beta release of BackBLAST v2
For several years, we have had a working BackBLAST v2 in alpha that was only available on the develop branch. Given that BackBLAST is not currently under active development, we have decided to push this version (with a few improvements) to main and to release it in beta for greater visibility.
This first beta release of v2.0.0 includes several major updates and feature changes compared to v1 of BackBLAST, including:
- The tool runs as a snakemake pipeline instead of a set of individual commands. This allows large numbers of genomes to be processed simultaneously.
- A single cli,
backblast, can be used to access and run the pipeline or individual utilities. - Installation is semi-automated via conda.
- In automating BackBLAST v2, we deprecated some functionality of v1, like identifying and visualizing gene clusters. See an old v1 release of you would still like to use this code.
Full Changelog (compared to the last v2 alpha version):
v2.0.0-alpha7...v2.0.0-beta1
Full Changelog (compared to v1.1):
v1.1...v2.0.0-beta1
We might continue development on BackBLAST to make a full v2.0.0 release someday, but for now, we hope these beta releases are helpful to the broader community. We hope to continue to provide updates from time to time.
Update installation
Updates the installation of BackBLAST for 2024. Installation on MacOS is also now supported.
Dependency updates
Basic update to tool dependencies so that BackBLAST is installable in 2022.
Dependency updates
Minor code cleanup; update of conda install and underlying dependencies.
Code refinement
Fixed minor bugs in v2.0.0-alpha3:
- Variable assignment issue that made
qcova required (rather than optional) setting - Environment path issue that prevented automated phylogeny generation
Also updated README.md with more current details.
Added query coverage support
- A minimum % query coverage threshold can now be set to filter reciprocal BLASTP hits
- Repo organization was streamlined.
BackBLASTis now calledbackblast. Support scripts are now hidden from the PATH and are accessed directly throughbackblastas modules.
Snakemake workflow
Pre-release of BackBLAST version 2. Reciprocal BLAST is now run across multiple samples in a snakemake pipeline, culminating in a visualization heatmap. See README for rough run instructions; more detailed documentation is on the way for the full version 2 release.
Re-pushing v2.0.0-alpha for a Zenodo DOI. No changes.
Snakemake workflow
Pre-release of BackBLAST version 2. Reciprocal BLAST is now run across multiple samples in a snakemake pipeline, culminating in a visualization heatmap. See README for rough run instructions; more detailed documentation is on the way for the full version 2 release.
Final release of version 1 code.
This is the last version of Backblast's original code base from when it was developed in 2015. It is being replaced by the latest code from 2023, version 2.0.