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    24 repositories

    • bgcflow

      Public
      Snakemake workflow for the analysis of biosynthetic gene clusters across large collections of genomes (pangenomes)
      genome-annotationgenome-analysisbiosynthetic-gene-clusterspangenome-pipeline
      Python
      •
      MIT License
      •9•36•35•3•Updated Dec 22, 2024Dec 22, 2024

    • Streptomyces_pangenome_ms

      Public
      Repository for the downstream analysis notebooks of Streptomyces pangenome article
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Dec 8, 2024Dec 8, 2024

    • G1034_NCBI_dataset

      Public
      A clean up version of the G1034 Actinomycetota genomes from NCBI
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Dec 7, 2024Dec 7, 2024

    • bgcflow_wrapper

      Public
      A snakemake wrapper and utility tools command line interface for BGCFlow.
      Python
      •
      MIT License
      •1•3•3•2•Updated Dec 6, 2024Dec 6, 2024

    • chatBGC_benchmark

      Public
      Benchmarking different LLMs for SQL-RAG query of BGC database
      Jupyter Notebook
      •0•0•0•3•Updated Nov 25, 2024Nov 25, 2024

    • chatBGC

      Public
      Ask questions about biosynthetic gene clusters in your genome dataset using Retrieval-Augmented Generation (RAG) from a BGCFlow run.
      Python
      •
      MIT License
      •1•1•0•0•Updated Aug 15, 2024Aug 15, 2024

    • bgcflow_dbt-duckdb

      Public
      An ELT framework based on DBT and DuckDB to process BGCFlow output tables
      Shell
      •1•2•3•0•Updated Jul 17, 2024Jul 17, 2024

    • antismash_db-schema_duckdb

      Public
      Initialize a local antiSMASH Database schema using DuckDB
      Python
      •
      MIT License
      •0•0•1•0•Updated Jul 4, 2024Jul 4, 2024

    • strainmap

      Public
      Map of the G1034 NPGM actinomycete strains published in NAR (https://doi.org/10.1093/nar/gkae523).
      HTML
      •0•0•0•0•Updated Jun 24, 2024Jun 24, 2024

    • bgcflow_report_demo

      Public
      BGCFlow report demo
      Python
      •0•0•0•0•Updated Apr 22, 2024Apr 22, 2024

    • saccharopolyspora_manuscript

      Public
      Jupyter notebook companion for the manuscript "BGCFlow: Systematic pangenome workflow for the analysis of biosynthetic gene clusters across large genomic datasets."
      HTML
      •
      MIT License
      •2•0•2•0•Updated Feb 16, 2024Feb 16, 2024

    • bgcflow_tutorial

      Public
      A short introduction to BGCflow data exploration
      0•0•0•0•Updated Feb 16, 2024Feb 16, 2024

    • trans-AT_G1034

      Public
      Analysis of TransAT PKS in the G1000 dataset
      HTML
      •0•0•0•0•Updated Jan 16, 2024Jan 16, 2024

    • meta_data_Figure1

      Public
      Notebook containing scripts to recreate Figure 1 of the G1034 paper
      Jupyter Notebook
      •0•0•0•0•Updated Jan 10, 2024Jan 10, 2024

    • Type1_Protospacers

      Public
      Script for the identification of type I(-C) protospacer sequences and evaluation of off-target sites.
      Jupyter Notebook
      •0•1•0•0•Updated Nov 13, 2023Nov 13, 2023

    • bigslice

      Public
      A highly scalable, user-interactive tool for the large scale analysis of Biosynthetic Gene Clusters data
      Python
      •
      GNU Affero General Public License v3.0
      •39•0•0•0•Updated Oct 9, 2023Oct 9, 2023

    • automlst-simplified-wrapper

      Public
      A fork of autoMLST with a simplified wrapper script bypassing additional organism selection.
      Python
      •3•0•1•0•Updated Aug 28, 2023Aug 28, 2023

    • umetaflow_tutorial

      Public
      Shell
      •2•0•1•0•Updated Jul 12, 2023Jul 12, 2023

    • Multiplexing_Scripts

      Public
      Scripts used for multiplexed base editing project
      Jupyter Notebook
      •0•0•0•0•Updated Jul 11, 2023Jul 11, 2023

    • snakemake-UmetaFlow

      Public
      Created for testing the metabolomics pipeline through snakemake
      Python
      •
      Apache License 2.0
      •0•2•0•0•Updated May 30, 2023May 30, 2023

    • arts_v3

      Public
      An experimental fork of ARTS2 (or 3?) running on python3. Use at your own risk. Forked from https://bitbucket.org/mehmetdirenc/arts_v3/src/master/
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Mar 3, 2023Mar 3, 2023

    • 2022-06-30-dtu

      Public
      BGCflow workshop during KAIST visit at DTU
      HTML
      •
      Other
      •0•0•0•0•Updated Jun 30, 2022Jun 30, 2022

    • BiG-SCAPE

      Public
      Similarity networks of biosynthetic gene clusters
      JavaScript
      •
      GNU Affero General Public License v3.0
      •27•0•0•0•Updated Apr 19, 2022Apr 19, 2022

    • AbsPresTree

      Public
      Create a phylogenetic tree with an absence/presence matrix of biosynthetic gene clusters
      Python
      •2•1•0•0•Updated Oct 26, 2020Oct 26, 2020