Repositories list

• SPARK

  Public
  Python

  •0•0•0•0•Updated Mar 4, 2026Mar 4, 2026

• MetasmithLibraries

  Public
  Python

  •1•0•0•2•Updated Feb 28, 2026Feb 28, 2026

• Metasmith

  Public
  Other

  •1•1•11•0•Updated Feb 24, 2026Feb 24, 2026

• Genome_announcements

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Feb 3, 2026Feb 3, 2026

• Copper_Binding

  Public
  R

  •0•0•0•0•Updated Jan 28, 2026Jan 28, 2026

• EPI300_genome_announcement

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Dec 4, 2025Dec 4, 2025

• Cellulase_Caulobacter_S-Layer_Display

  Public
  raw data and code for analysis and visualisation of associated manuscript

  0•0•0•0•Updated Nov 21, 2025Nov 21, 2025

• FabFos

  Public
  A pooled fosmid assembly pipeline in python, driven by Snakemake

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •3•1•2•0•Updated Oct 14, 2025Oct 14, 2025

• Nostoc_metagenome_announcement

  Public
  Python

  •0•0•0•0•Updated Sep 23, 2025Sep 23, 2025

• SynC_genome_announcement

  Public
  0•0•0•0•Updated Sep 14, 2025Sep 14, 2025

• CB2A_genome_announcement

  Public
  Python

  •0•0•0•0•Updated Sep 13, 2025Sep 13, 2025

• genome_qc

  Public
  in-house genome QC workflow

  Python

  •

  GNU General Public License v3.0

  •0•0•1•1•Updated Sep 12, 2025Sep 12, 2025

• FAST

  Public
  FAST Aligner

  C++

  •1•6•2•0•Updated Jul 17, 2025Jul 17, 2025

• NESAP_marine_heatwaves

  Public
  This is the code repository for our manuscript highlighting the effects of marine heatwaves on food webs and particle export in the Northeast Subarctic Pacific …

  RMarkdown

  •1•0•0•0•Updated Jul 8, 2025Jul 8, 2025

• SABer

  Public
  SAG Anchored Binner

  Python

  •

  GNU General Public License v3.0

  •2•2•6•1•Updated Jun 13, 2025Jun 13, 2025

• MetaPathways

  Public
  A modular pipeline for constructing Pathway/Genome Databases from environmental sequence information

  Perl

  •7•13•0•0•Updated Apr 4, 2025Apr 4, 2025

• TreeSAPP

  Public
  A Python package for gene-centric taxonomic and functional classification using phylogenetic placement

  bioinformaticsphylogeneticsmicrobial-genomics

  bioinformaticsphylogeneticsmicrobial-genomics

  Python

  •

  GNU General Public License v3.0

  •4•26•19•3•Updated Sep 3, 2024Sep 3, 2024

• samsum

  Public
  A light-weight python package for summarizing sequence coverage from SAM and BAM files

  bioinformaticssequence-alignment

  bioinformaticssequence-alignment

  Python

  •

  GNU General Public License v3.0

  •3•7•8•1•Updated Sep 3, 2024Sep 3, 2024

• LCAStar

  Public
  Alternative taxonomic consensus algorithms based on the NCBI taxonomy tree

  HTML

  •

  GNU General Public License v3.0

  •4•16•0•0•Updated May 29, 2024May 29, 2024

• python_starter_template

  Public
  Python

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated Oct 17, 2023Oct 17, 2023

• Fosmid-walk

  Public
  Python

  •1•0•0•0•Updated Oct 5, 2023Oct 5, 2023

• Limes-compute-modules

  Public
  Python

  •2•0•0•0•Updated Sep 14, 2023Sep 14, 2023

• Limes-x

  Public
  Python

  •1•1•3•0•Updated Aug 6, 2023Aug 6, 2023

• MAGSplitter

  Public
  Standalone script to split a Metapathways metagenome output by MAGs

  Python

  •1•0•0•0•Updated Jul 27, 2023Jul 27, 2023

• mlLGPR

  Public
  Metabolic pathway inference using multi-label classification with rich pathway features

  bioinformaticsmetagenomicslogistic-regression+ 5

  bioinformaticsmetagenomicslogistic-regressionmulti-label-learningpathway-predictionmetacycbiocycpathway-tools

  Python

  •

  GNU General Public License v3.0

  •0•7•2•1•Updated Jul 6, 2023Jul 6, 2023

• OMZ_SAG_Compendium_Figures

  Public
  0•0•0•0•Updated Mar 22, 2023Mar 22, 2023

• MetaPathwaysGUI

  Public
  C++

  •0•3•0•0•Updated Jan 19, 2023Jan 19, 2023

• sgRNAble

  Public
  Python

  •

  GNU General Public License v3.0

  •1•1•3•2•Updated Dec 8, 2022Dec 8, 2022

• MetaTaxa

  Public
  0•0•0•0•Updated Aug 2, 2022Aug 2, 2022

• RefPkgs

  Public
  Repository for TreeSAPP reference packages

  Python

  •

  GNU General Public License v3.0

  •3•1•2•1•Updated Apr 16, 2022Apr 16, 2022