Science Score: 75.0%
This score indicates how likely this project is to be science-related based on various indicators:
-
✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 5 DOI reference(s) in README -
✓Academic publication links
Links to: zenodo.org -
○Academic email domains
-
✓Institutional organization owner
Organization kalan-lab has institutional domain (kalanlab.mmi.wisc.edu) -
○JOSS paper metadata
-
○Scientific vocabulary similarity
Low similarity (7.3%) to scientific vocabulary
Keywords
Repository
lsaBGC - suite for pan-BGC-omics analysis
Basic Info
Statistics
- Stars: 19
- Watchers: 2
- Forks: 2
- Open Issues: 1
- Releases: 16
Topics
Metadata Files
README.md
lsaBGC-Pan
lsaBGC-Pan - mine the pan-BGC-ome of a microbial taxon for biosynthetic golden nuggets.
lsaBGC-Pan reconfigures lsaBGC for easier installation via either Bioconda or Docker and features a new workflow bearing the same name as the repo. In addition to easier usability, there are some new analytical modules -e.g. (de-)association testing of BGC ortholog groups and GCFs and an improved framework for inferring horizontal transfer.
Manuscript:
Evolutionary investigations of the biosynthetic diversity in the skin microbiome using lsaBGC. Microbial Genomics 2023. Rauf Salamzade, J.Z. Alex Cheong, Shelby Sandstrom, Mary Hannah Swaney, Reed M. Stubbendieck, Nicole Lane Starr, Cameron R. Currie, Anne Marie Singh, and Lindsay R. Kalan
Key Highlights:
✔️ Works for both fungi & bacteria
✔️ Allows for joint analysis of antiSMASH & GECCO BGC predictions (in analysis of Streptomyces olivaceus - this leads to a 42.4% increase in distinct GCFs to using antiSMASH alone)
✔️ Better consideration for incomplete BGCs due to assembly fragmentation
✔️ New analytical features including: (1) genome-wide association testing of orthogroups with GCF co-occurence & (2) improved assessment of horizontal transfer for BGC-associated orthogroups
✔️ Improved consolidated spreadsheet that is easier to assess
✔️ Support for small scale (< 30 genomes) analysis on laptop with minimal databases (~5 GB).
✔️ Bioconda installation tested on both macOS & Linux with easy-to-use Docker image & wrapper script also coming soon!
✔️ BSD-3 License & no uploading of data to webservers = support for industry research
Documentation:
Documentation and three separate tutorials showing application to:
- A small set of 7 Cutibacterium avidum and Cutibacterium acnes genomes (test dataset included with repo)
- A set of 12 Aspergillus flavus genomes (fungal showcase)
- A set of 23 distinct Streptomyces olivaceus strains (shows joint AntiSMASH + GECCO analysis)
can be found on the wiki at: https://github.com/Kalan-Lab/lsaBGC-Pan/wiki
Example Commands:
Perform analysis using a directory of AntiSMASH results as input:
bash
lsaBGC-Pan -a AntiSMASH_Results/ -o Pan_Results/ -c 10
Provide a directory of AntiSMASH results as input and incorporate GECCO BGC predictions as well:
bash
lsaBGC-Pan -a AntiSMASH_Results/ -o Pan_Results/ -c 10 -rg
Provide a directory of genomes in FASTA format for GECCO-based BGC predictions and analysis (only works for bacteria):
bash
lsaBGC-Pan -g Directory_of_Genomes_in_FASTA/ -o Pan_Results/ -c 10
Owner
- Name: Kalan-Lab
- Login: Kalan-Lab
- Kind: organization
- Location: University of Wisconsin-Madison
- Website: kalanlab.mmi.wisc.edu
- Repositories: 2
- Profile: https://github.com/Kalan-Lab
A Place to Collaborate
Citation (CITATION.cff)
cff-version: 1.2.0 message: "If you use this software, please cite the lsaBGC manuscript published in Microbial Genomics." authors: - family-names: "Salamzade" given-names: "Rauf" orcid: "https://orcid.org/0000-0002-1923-5948" - family-names: "Kalan" given-names: "Lindsay" orcid: "https://orcid.org/0000-0003-4980-5128" title: "lsaBGC-Pan" version: 1.1.4 date-released: 2025-06-29 url: "https://github.com/Kalan-Lab/lsaBGC-Pan"
GitHub Events
Total
- Create event: 4
- Release event: 4
- Issues event: 3
- Watch event: 6
- Issue comment event: 13
- Push event: 16
- Pull request event: 1
- Gollum event: 8
Last Year
- Create event: 4
- Release event: 4
- Issues event: 3
- Watch event: 6
- Issue comment event: 13
- Push event: 16
- Pull request event: 1
- Gollum event: 8
Issues and Pull Requests
Last synced: 4 months ago
All Time
- Total issues: 1
- Total pull requests: 1
- Average time to close issues: 4 days
- Average time to close pull requests: less than a minute
- Total issue authors: 1
- Total pull request authors: 1
- Average comments per issue: 4.0
- Average comments per pull request: 0.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 1
- Pull requests: 1
- Average time to close issues: 4 days
- Average time to close pull requests: less than a minute
- Issue authors: 1
- Pull request authors: 1
- Average comments per issue: 4.0
- Average comments per pull request: 0.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- raufs (7)
- amizeranschi (1)
- Arin1643 (1)
- MHassanSaeed (1)
Pull Request Authors
- raufs (3)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- continuumio/miniconda3 latest build