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    29 repositories

    • sunbeam

      Public
      A robust, extensible metagenomics pipeline
      reproducible-researchmetagenomicssnakemake
      Python
      •40•166•15•2•Updated Aug 15, 2024Aug 15, 2024

    • sbx_gene_clusters

      Public
      Python
      •5•2•1•1•Updated Aug 9, 2024Aug 9, 2024

    • sbx_virus_id

      Public
      Python
      •0•0•4•0•Updated Aug 8, 2024Aug 8, 2024

    • 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_kraken

      Public
      Extension for running kraken2 and kraken2-biom
      Python
      •1•0•1•0•Updated Jun 25, 2024Jun 25, 2024

    • sbx_mapping

      Public
      Extension to map reads against a set of reference genomes
      Python
      •1•0•1•0•Updated Jun 25, 2024Jun 25, 2024

    • sbx_coassembly

      Public
      Sunbeam extension to co-assemble metagenomic reads using Megahit
      Python
      •2•0•1•0•Updated Mar 29, 2024Mar 29, 2024

    • sbx_assembly

      Public
      Sunbeam extension for assembly (megahit) and annotation (prodigal)
      Python
      •0•0•0•1•Updated Mar 29, 2024Mar 29, 2024

    • sbx_template

      Public template
      Template for Sunbeam extensions.
      Python
      •2•3•0•0•Updated Mar 26, 2024Mar 26, 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_test_action

      Public
      GH Action for testing sunbeam extensions
      0•0•0•0•Updated Nov 15, 2023Nov 15, 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-classificationsunbeamkrakenhll
      2•3•0•0•Updated Dec 14, 2018Dec 14, 2018

    • sbx_silva18S

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

    • sbx_shortbred

      Public
      0•0•0•0•Updated Dec 13, 2018Dec 13, 2018

    • sbx_contigs

      Public
      R
      •1•1•0•0•Updated Nov 21, 2018Nov 21, 2018

    • sunbeam-poster

      Public
      Poster for ASM NGS 2018
      0•0•0•0•Updated Oct 9, 2018Oct 9, 2018

    • sbx_fungi_mapping

      Public
      0•0•0•0•Updated May 2, 2018May 2, 2018

    • sbx_igv

      Public
      IGV extension for Sunbeam
      Python
      •0•0•0•0•Updated May 2, 2018May 2, 2018