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    35 repositories

    • sbx_assembly

      Public
      Sunbeam extension for assembly (megahit) and annotation (prodigal)
      Python
      •1•0•0•1•Updated Aug 11, 2026Aug 11, 2026

    • sbx_cenote_taker

      Public
      Python
      •1•0•3•1•Updated Aug 11, 2026Aug 11, 2026

    • sbx_genomad

      Public
      Run geNomad end-to-end pipeline
      Python
      •0•0•0•2•Updated Aug 11, 2026Aug 11, 2026

    • sbx_gene_clusters

      Public
      Python
      •5•2•1•2•Updated Aug 10, 2026Aug 10, 2026

    • sunbeam

      Public
      A robust, extensible metagenomics pipeline
      snakemakereproducible-researchmetagenomics
      snakemakereproducible-researchmetagenomics
      Python
      •45•177•24•11•Updated Aug 10, 2026Aug 10, 2026

    • sbx_shotgun_unifrac

      Public
      Sunbeam extension for assigning metagenomic reads to a full bacterial phylogeny
      Python
      •0•0•2•2•Updated Aug 10, 2026Aug 10, 2026

    • sbx_template

      Public template
      Template for Sunbeam extensions.
      Python
      •3•3•0•4•Updated Aug 10, 2026Aug 10, 2026

    • sbx_sga

      Public
      A Sunbeam extension for Single Genome Assembly
      Python
      •3•0•3•2•Updated Aug 10, 2026Aug 10, 2026

    • sbx_baqlava

      Public
      Runs BAQLaVa on decontaminated reads.
      Python
      •0•0•0•5•Updated Aug 10, 2026Aug 10, 2026

    • sbx_coassembly

      Public
      Sunbeam extension to co-assemble metagenomic reads using Megahit
      Python
      •2•0•1•1•Updated Aug 10, 2026Aug 10, 2026

    • sbx_kraken

      Public
      Extension for running kraken2 and kraken2-biom
      Python
      •3•0•1•4•Updated Aug 10, 2026Aug 10, 2026

    • sbx_mapping

      Public
      Extension to map reads against a set of reference genomes
      Python
      •1•0•0•1•Updated Aug 10, 2026Aug 10, 2026

    • sbx_test_action

      Public
      GH Action for testing sunbeam extensions
      0•0•0•3•Updated Jun 22, 2026Jun 22, 2026

    • condabot

      Public
      Automate dependency upgrades
      0•0•0•1•Updated Dec 15, 2025Dec 15, 2025

    • sbx_induceome

      Public
      Helps with identifying induced phage in well prepared samples
      Python
      •0•1•1•1•Updated Jun 10, 2025Jun 10, 2025

    • sbx_vsearch

      Public
      Sunbeam extension for Vsearch (https://github.com/torognes/vsearch)
      Python
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Aug 6, 2024Aug 6, 2024

    • sbx_metaphlan4

      Public
      Sunbeam extension for metaphlan 4 (compatible with sunbeam 4)
      Python
      •1•0•1•0•Updated Aug 5, 2024Aug 5, 2024

    • sbx_demic

      Public
      A sunbeam extension to run DEMIC, a peak-to-trough ratio generator for bacteria short-reads
      Perl
      •1•3•4•3•Updated Feb 8, 2024Feb 8, 2024

    • sbx_genome_assembly

      Public
      Python
      •3•0•2•1•Updated Dec 21, 2023Dec 21, 2023

    • sbx_phase_finder

      Public
      Python
      •0•0•1•0•Updated Nov 8, 2023Nov 8, 2023

    • sbx_metaspades_example

      Public
      Example Sunbeam extension for assembly with metaspades.
      0•0•0•0•Updated May 31, 2022May 31, 2022

    • sbx_kaiju

      Public
      Kaiju metagenomics classifier for Sunbeam
      GNU General Public License v3.0
      •3•0•2•0•Updated Apr 6, 2021Apr 6, 2021

    • sunbeam-labs.github.io

      Public
      CSS
      •2•0•3•1•Updated Feb 14, 2020Feb 14, 2020

    • sbx_spades

      Public
      1•0•1•0•Updated Dec 13, 2019Dec 13, 2019

    • sbx_anvio

      Public
      0•0•0•0•Updated Dec 13, 2019Dec 13, 2019

    • sbx_subsample

      Public
      Sunbeam extension to subsample reads after quality control
      GNU General Public License v3.0
      •0•0•0•0•Updated Dec 12, 2019Dec 12, 2019

    • sbx_report

      Public
      Generates a final report, with figures, from a Sunbeam run
      HTML
      •1•3•5•0•Updated Dec 11, 2019Dec 11, 2019

    • sbx_metaphlan

      Public
      Sunbeam extension for running MetaPhlAn
      3•0•3•1•Updated Jan 10, 2019Jan 10, 2019

    • sbx_krakenhll

      Public
      snakemakemetagenomic-classificationsunbeam
      snakemakemetagenomic-classificationsunbeamkrakenhll
      1•3•0•0•Updated Dec 14, 2018Dec 14, 2018

    • sbx_silva18S

      Public
      0•0•0•0•Updated Dec 14, 2018Dec 14, 2018
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