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@NBChub

NBCHub

Repositories for analyzing large scale datasets for natural products discovery developed at DTU Biosustain

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  1. bgcflow bgcflow Public

    Snakemake workflow for the analysis of biosynthetic gene clusters across large collections of genomes (pangenomes)

    Python 35 9

  2. bgcflow_wrapper bgcflow_wrapper Public

    A snakemake wrapper and utility tools command line interface for BGCFlow.

    Python 3 1

  3. snakemake-UmetaFlow snakemake-UmetaFlow Public

    Created for testing the metabolomics pipeline through snakemake

    Python 2

  4. bgcflow_dbt-duckdb bgcflow_dbt-duckdb Public

    An ELT framework based on DBT and DuckDB to process BGCFlow output tables

    Shell 2 1

  5. AbsPresTree AbsPresTree Public

    Forked from OmkarSaMo/AbsPresTree

    Create a phylogenetic tree with an absence/presence matrix of biosynthetic gene clusters

    Python 1

  6. Type1_Protospacers Type1_Protospacers Public

    Script for the identification of type I(-C) protospacer sequences and evaluation of off-target sites.

    Jupyter Notebook 1

Repositories

Showing 10 of 24 repositories
  • G1034_NCBI_dataset Public

    A clean up version of the G1034 Actinomycetota genomes from NCBI

    NBChub/G1034_NCBI_dataset’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Nov 15, 2024
  • Streptomyces_pangenome_ms Public

    Repository for the downstream analysis notebooks of Streptomyces pangenome article

    NBChub/Streptomyces_pangenome_ms’s past year of commit activity
    Jupyter Notebook 0 0 0 0 Updated Oct 15, 2024
  • bgcflow Public

    Snakemake workflow for the analysis of biosynthetic gene clusters across large collections of genomes (pangenomes)

    NBChub/bgcflow’s past year of commit activity
    Python 35 MIT 9 34 (2 issues need help) 3 Updated Oct 9, 2024
  • chatBGC_benchmark Public

    Benchmarking different LLMs for SQL-RAG query of BGC database

    NBChub/chatBGC_benchmark’s past year of commit activity
    Jupyter Notebook 0 0 0 0 Updated Aug 28, 2024
  • chatBGC Public

    Ask questions about biosynthetic gene clusters in your genome dataset using Retrieval-Augmented Generation (RAG) from a BGCFlow run.

    NBChub/chatBGC’s past year of commit activity
    Python 1 MIT 1 0 0 Updated Aug 15, 2024
  • bgcflow_dbt-duckdb Public

    An ELT framework based on DBT and DuckDB to process BGCFlow output tables

    NBChub/bgcflow_dbt-duckdb’s past year of commit activity
    Shell 2 1 3 0 Updated Jul 17, 2024
  • antismash_db-schema_duckdb Public

    Initialize a local antiSMASH Database schema using DuckDB

    NBChub/antismash_db-schema_duckdb’s past year of commit activity
    Python 0 MIT 0 1 0 Updated Jul 4, 2024
  • strainmap Public

    Map of the G1034 NPGM actinomycete strains published in NAR (https://doi.org/10.1093/nar/gkae523).

    NBChub/strainmap’s past year of commit activity
    HTML 0 0 0 0 Updated Jun 24, 2024
  • bgcflow_wrapper Public

    A snakemake wrapper and utility tools command line interface for BGCFlow.

    NBChub/bgcflow_wrapper’s past year of commit activity
    Python 3 MIT 1 3 1 Updated Jun 20, 2024
  • bgcflow_report_demo Public

    BGCFlow report demo

    NBChub/bgcflow_report_demo’s past year of commit activity
    Python 0 0 0 0 Updated Apr 22, 2024
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