Repositories list

• sunbeam

  Public
  A robust, extensible metagenomics pipeline

  reproducible-researchmetagenomicssnakemake

  Python

  •43•171•12•6•Updated Jul 8, 2025Jul 8, 2025

• sbx_sga

  Public
  A Sunbeam extension for Single Genome Assembly

  Python

  •3•0•5•3•Updated Jul 7, 2025Jul 7, 2025

• sbx_shotgun_unifrac

  Public
  Sunbeam extension for assigning metagenomic reads to a full bacterial phylogeny

  Python

  •0•0•2•2•Updated Jul 7, 2025Jul 7, 2025

• sbx_template

  Public template
  Template for Sunbeam extensions.

  Python

  •2•3•0•2•Updated Jul 7, 2025Jul 7, 2025

• sbx_coassembly

  Public
  Sunbeam extension to co-assemble metagenomic reads using Megahit

  Python

  •2•0•1•1•Updated Jul 7, 2025Jul 7, 2025

• sbx_kraken

  Public
  Extension for running kraken2 and kraken2-biom

  Python

  •1•0•1•1•Updated Jul 7, 2025Jul 7, 2025

• sbx_mapping

  Public
  Extension to map reads against a set of reference genomes

  Python

  •1•0•0•1•Updated Jul 7, 2025Jul 7, 2025

• sbx_assembly

  Public
  Sunbeam extension for assembly (megahit) and annotation (prodigal)

  Python

  •0•0•0•1•Updated Jul 7, 2025Jul 7, 2025

• sbx_test_action

  Public
  GH Action for testing sunbeam extensions

  0•0•0•0•Updated Jul 2, 2025Jul 2, 2025

• sbx_gene_clusters

  Public
  Python

  •5•2•1•2•Updated Jun 30, 2025Jun 30, 2025

• sbx_induceome

  Public
  Helps with identifying induced phage in well prepared samples

  Python

  •0•1•1•1•Updated Jun 10, 2025Jun 10, 2025

• condabot

  Public
  Automate dependency upgrades

  0•0•0•1•Updated Jun 2, 2025Jun 2, 2025

• sbx_virus_id

  Public
  Python

  •0•0•4•0•Updated Nov 20, 2024Nov 20, 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_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+ 1krakenhll

  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