Repositories list

• DRAM

  Public
  Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes

  bioinformaticsannotationgenomics+ 5

  bioinformaticsannotationgenomicsmetagenomicsmicrobiomeviral-genomicsviral-metagenomicsmetagenome-assembled-genomes

  Python

  •

  GNU General Public License v3.0

  •6262 forks•332332 stars•122122 issues•33 pull requests•Updated Apr 30, 2026Apr 30, 2026

• dram-viz

  Public
  A library for visualizing the output of DRAM v2

  Python

  •

  MIT License

  •00 forks•22 stars•33 issues•00 pull requests•Updated Mar 6, 2026Mar 6, 2026

• Rule-Parser

  Public
  Rule Parser for various DRAM tooling

  Python

  •

  GNU General Public License v3.0

  •00 forks•11 star•00 issues•00 pull requests•Updated Mar 4, 2026Mar 4, 2026

• server-scripts

  Public
  Central location for tools and scripts for the lab

  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Oct 18, 2025Oct 18, 2025

• catechin_incubations

  Public
  R

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Nov 7, 2024Nov 7, 2024

• JGI-API-Request

  Public
  Python script is designed to fetch and process genomic data from the Joint Genome Institute (JGI) API, allowing users to request file downloads programmatically…

  Python

  •11 fork•55 stars•00 issues•00 pull requests•Updated Jul 2, 2024Jul 2, 2024

• Protpipeliner

  Public
  This script combines MUSCLE, GBLOCKS, Prottest and RaxML for an efficient and streamlined method of building trees.

  Python

  •00 forks•11 star•00 issues•00 pull requests•Updated May 14, 2024May 14, 2024

• CAMPER

  Public
  This is a repository for CAMPER.

  Python

  •

  GNU General Public License v3.0

  •00 forks•1717 stars•22 issues•00 pull requests•Updated Mar 18, 2024Mar 18, 2024

• stordalen_polyphenols_paper

  Public
  HTML

  •00 forks•00 stars•00 issues•00 pull requests•Updated Feb 23, 2024Feb 23, 2024

• AD_CERC

  Public
  00 forks•00 stars•00 issues•00 pull requests•Updated Sep 19, 2023Sep 19, 2023

• kb_DRAM

  Public
  A Kbase app for DRAM

  Python

  •

  MIT License

  •33 forks•11 star•33 issues•00 pull requests•Updated Jun 24, 2023Jun 24, 2023

• prodigal-recoding

  Public
  Fork of Prodigal Gene Prediction Software to introduce recoding of stop codons

  C

  •

  GNU General Public License v3.0

  •9494 forks•00 stars•00 issues•00 pull requests•Updated Apr 1, 2023Apr 1, 2023

• join_asvbins

  Public
  Python

  •

  GNU General Public License v3.0

  •00 forks•22 stars•11 issue•00 pull requests•Updated Dec 8, 2022Dec 8, 2022

• emerge_pipline

  Public
  The pipline for the folks at emerge, they will want it eventualy

  Python

  •22 forks•00 stars•00 issues•00 pull requests•Updated Aug 29, 2022Aug 29, 2022

• columbia_river

  Public
  GitHub Repository of code used for the publication titled: Genome-resolved metaproteomics decodes the microbial and viral contributions to coupled carbon and ni…

  Python

  •

  GNU General Public License v3.0

  •11 fork•00 stars•00 issues•00 pull requests•Updated Jun 1, 2022Jun 1, 2022

• sporulation_utils

  Public
  These tools help us study sporulation AMGs with DRAM-v and DRAM

  Python

  •11 fork•00 stars•00 issues•00 pull requests•Updated Feb 15, 2022Feb 15, 2022