Repositories list

• Fungi_BFD

  Public
  Fungi Big-Fun-Data

  Python

  •00 forks•22 stars•11 issue•00 pull requests•Updated Aug 20, 2026Aug 20, 2026

• Batrachochytrium_EB_MS_compare

  Public
  Analysis of EB run of MS on Batrachochytrium stage and species

  HTML

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 20, 2026Aug 20, 2026

• Batrachochytrium_GNPS1_compare

  Public
  Contrasting Metabolomics data from Batrachochytrium

  HTML

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 20, 2026Aug 20, 2026

• nf_funannotate1

  Public
  Annotation strategy for Eukaryotic genomes with auto incorporation of public evidence

  Nextflow

  •

  MIT License

  •00 forks•00 stars•33 issues•00 pull requests•Updated Aug 19, 2026Aug 19, 2026

• Rhodotorula_pheno_MS

  Public
  Rhodotorula phenotype and MS data cleanup and re-run

  HTML

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 19, 2026Aug 19, 2026

• NovInvenio

  Public
  HTML

  •00 forks•11 star•00 issues•00 pull requests•Updated Aug 19, 2026Aug 19, 2026

• AAFTF

  Public
  Automatic Assembly For The Fungi

  Python

  •

  MIT License

  •66 forks•2727 stars•99 issues•00 pull requests•Updated Aug 19, 2026Aug 19, 2026

• nf_aaftf

  Public
  Nextflow workflow for running AAFTF (Automatic Assembly For The Fungi)

  Nextflow

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 18, 2026Aug 18, 2026

• RelocaTE3

  Public
  ReLocaTE code for identifying Transposons (TE) in genomes using re-sequencing data

  Python

  •

  MIT License

  •00 forks•33 stars•11 issue•00 pull requests•Updated Aug 14, 2026Aug 14, 2026

• orthoSynAssign

  Public
  Assign orthologs within many-many groups with synteny

  Python

  •

  GNU General Public License v3.0

  •11 fork•55 stars•00 issues•00 pull requests•Updated Aug 13, 2026Aug 13, 2026

• Rhodotorula_MS2_pheno_explore

  Public
  MS2 metabolite-color phenotype analysis pipeline for Rhodotorula strains

  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 13, 2026Aug 13, 2026

• BFD_dashboard

  Public
  Web interface to BFD through generated HTML and Chat

  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 10, 2026Aug 10, 2026

• SSF_PRB_Fungal_Genomes

  Public
  Powder River Basin cultured fungal genomes

  HTML

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 9, 2026Aug 9, 2026

• stajichlab.github.io

  Public
  Stajich Lab Website

  genomefungimycology

  genomefungimycology

  HTML

  •

  BSD 3-Clause "New" or "Revised" License

  •443443 forks•00 stars•00 issues•00 pull requests•Updated Aug 7, 2026Aug 7, 2026

• Coccidioides_Assembly_LongRead

  Public
  Long read assembly dataset pipeline and examination

  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 6, 2026Aug 6, 2026

• nf_phyling

  Public
  Nextflow pipeline for multi-locus fungal phylogenomics: PHYling → PhyKIT → ModelTest-NG → IQ-TREE 3 → RAxML-NG

  Nextflow

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 29, 2026Jul 29, 2026

• fungenome-classifier

  Public
  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 28, 2026Jul 28, 2026

• Phyling

  Public
  Phyling: phylogenetic inference from annotated genomes

  pythonphylogeneticssoftware+ 3

  pythonphylogeneticssoftwarehidden-markov-modelphylogenomicsorthology

  Python

  •

  MIT License

  •44 forks•3232 stars•33 issues•77 pull requests•Updated Jul 27, 2026Jul 27, 2026

• HeavyMetal_rhodotorula

  Public
  Attempt 2 test to unify Metal + Metabolite + Genotype

  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 13, 2026Jul 13, 2026

• Rhodotorula_StrainDB

  Public
  Strain database with metadata query/import support

  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 1, 2026Jul 1, 2026

• Cramer_Vellanki_scRNA_Biofilm

  Public
  scRNA Afum analysis

  Shell

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jun 30, 2026Jun 30, 2026

• adhesionPred

  Public
  Adhesion protein prediction

  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•66 pull requests•Updated Jun 27, 2026Jun 27, 2026

• Cramer_Kordana_HrmA_sector

  Public
  HTML

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jun 12, 2026Jun 12, 2026

• Trebouxia_Schmitt

  Public
  Duplication analysis

  Shell

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jun 11, 2026Jun 11, 2026

• Afumigatus_RefStrains

  Public
  Reference A. fumigatus strain panel

  Shell

  •00 forks•11 star•00 issues•00 pull requests•Updated Jun 10, 2026Jun 10, 2026

• APIBA_Melipona_favosa_Microbiome_Analysis

  Public
  Metagenome and Amplicon for stingless bee pilot project

  HTML

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jun 1, 2026Jun 1, 2026

• HoganLab_Dhansenii_CDA1_annotation

  Public
  Annotation of Debaryomyces hansenii CDA1

  AMPL

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 19, 2026May 19, 2026

• Fungi_5k

  Public
  Fungi5k dataset analysis

  Python

  •11 fork•11 star•00 issues•00 pull requests•Updated Apr 22, 2026Apr 22, 2026

• SSF_contrast

  Public
  Subsurface Fungi Genomes Contrast

  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 17, 2026Apr 17, 2026

• Antarctica_Endolithic_Eukaryotic_MAG

  Public
  Eukaryotic MAGs from Endolithic metagenome sampling

  Shell

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 8, 2026Apr 8, 2026