Repositories list

• PHYling

  Public
  PHYling pipeline for species tree building from annotated genomes (see https://github.com/stajichlab/AAFTF and https://github.com/nextgenusfs/funannotate for assembly and annotation steps)

  bioinformaticsngssequencing+ 3markersgenomesphylogenetic-analyses

  Python

  •

  MIT License

  •3•7•6•0•Updated Feb 6, 2025Feb 6, 2025

• DhingraLab_Afum_ncRNA

  Public
  A.fumigatus ncRNA analysis

  Shell

  •0•0•0•0•Updated Feb 6, 2025Feb 6, 2025

• RolshausenLab_Aspergillus_DatePalm

  Public
  Aspergillus tubingensis DFA genome sequencing and annotation

  Shell

  •

  MIT License

  •1•1•0•0•Updated Feb 6, 2025Feb 6, 2025

• ExtremeRhodotorula_RefGenomes

  Public
  Reference Genome Assembly and Annotation for Rhodotorula genomes in "Extreme Rhodotorula" project

  Shell

  •

  MIT License

  •0•0•0•0•Updated Feb 5, 2025Feb 5, 2025

• SOP_data

  Public
  Standard Operating Procedures

  MIT License

  •0•0•5•0•Updated Feb 4, 2025Feb 4, 2025

• stajichlab.github.io

  Public
  Stajich Lab Website

  genomefungimycology

  HTML

  •

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

  •326•0•0•0•Updated Feb 3, 2025Feb 3, 2025

• PopGenomics_Rhodotorula_mucilaginosa_NRRLY2510

  Public
  Rhodotorula mucilaginosa population genomics with ref strain NRRL Y-2510

  R

  •

  MIT License

  •0•0•0•0•Updated Feb 3, 2025Feb 3, 2025

• PopGenomics_template

  Public template
  Template for Population Genomics variant calling

  Shell

  •

  MIT License

  •2•2•2•0•Updated Jan 28, 2025Jan 28, 2025

• AAFTF

  Public
  Automatic Assembly For The Fungi

  Python

  •

  MIT License

  •4•19•10•0•Updated Jan 23, 2025Jan 23, 2025

• Fungi_5k

  Public
  Fungi5k dataset analysis

  Python

  •0•0•0•0•Updated Jan 23, 2025Jan 23, 2025

• PopGenomics_Afumigatus_Global

  Public
  A. fumigatus population genomics 2021 relaunch

  HTML

  •

  MIT License

  •0•0•0•0•Updated Jan 22, 2025Jan 22, 2025

• moss_mycobiome

  Public
  Repository for all code related to moss biocrust mycobiome studies across an aridity gradient including AMF specific analyses and general fungal diversity.

  HTML

  •0•0•0•0•Updated Jan 15, 2025Jan 15, 2025

• PopGenomics_Cimmitis

  Public
  Population Genomics and CNV analysis of C. immitis strains

  HTML

  •

  MIT License

  •0•0•0•0•Updated Jan 10, 2025Jan 10, 2025

• MATPredict

  Public
  This repository is dedicated to the development of a tool that can predict MAT loci in fungi.

  Python

  •0•0•0•0•Updated Dec 17, 2024Dec 17, 2024

• PopGenomics_Asocialis_CCGP

  Public
  Population Genomics for the A.socialis CCGP project

  R

  •

  MIT License

  •0•0•0•0•Updated Dec 11, 2024Dec 11, 2024

• PopGenomics_Acarospora_socialis_HerbariumSamples

  Public
  Population genomics of A. socialis from Herbarium specimens

  Shell

  •

  MIT License

  •0•0•0•0•Updated Dec 10, 2024Dec 10, 2024

• Compgenomics_Ecrusticola

  Public
  This repo is dedicated to the assembly, annotation, and comparative genomic analysis of Exophiala crusticola (the architypal biocrust black yeast).

  Python

  •0•0•0•0•Updated Oct 29, 2024Oct 29, 2024

• KassonLab_Nectriaceae

  Public
  Nectriaceae genomes project with Matt Kasson lab (WVU)

  R

  •

  MIT License

  •0•0•0•0•Updated Oct 27, 2024Oct 27, 2024

• PopGenomics_Afumigatus_CEA10

  Public
  Explore CEA10 Strain variation

  R

  •

  MIT License

  •0•0•0•0•Updated Oct 17, 2024Oct 17, 2024

• Acarospora_socialis_annotation

  Public
  Annotation of Acarospora socialis genome for CCGP

  Shell

  •0•0•0•0•Updated Sep 25, 2024Sep 25, 2024

• funannotate_template

  Public template
  Project template for doing a funannotate annotation set

  Shell

  •

  MIT License

  •1•1•0•0•Updated Sep 25, 2024Sep 25, 2024

• ExtremeRhodotorula_Hybrid_Diploid

  Public
  Investigating potential diploid/hybrid strains

  Python

  •0•0•0•0•Updated Sep 24, 2024Sep 24, 2024

• ExtremeRhodotorula_DraftGenomes

  Public
  Draft genomes from short read data

  Shell

  •

  MIT License

  •0•0•0•0•Updated Sep 19, 2024Sep 19, 2024

• Biocrust_fungi_hybrid_asm_annotation

  Public
  Nanopore and illumina sequences for biocrust fungal isolates

  R

  •

  MIT License

  •1•0•0•0•Updated Sep 13, 2024Sep 13, 2024

• Y1000_orthologs

  Public
  Compare and Build Orthogroups for Y1000 dataset and compare to YGOB

  Python

  •

  MIT License

  •0•0•0•0•Updated Sep 2, 2024Sep 2, 2024

• TaniaK_CF_Exophiala_dermatitidis

  Public
  Archiving repo from paper.

  HTML

  •2•0•0•0•Updated Aug 13, 2024Aug 13, 2024

• stajichlab.github.io-v2

  Public archive
  lab site test

  HTML

  •2•0•0•1•Updated Aug 2, 2024Aug 2, 2024

• RelocaTE3

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

  Python

  •

  MIT License

  •1•3•4•0•Updated Jul 13, 2024Jul 13, 2024

• Trebouxia_Schmitt

  Public
  Duplication analysis

  Shell

  •0•0•0•0•Updated Jul 7, 2024Jul 7, 2024

• Comparative_pipeline

  Public
  Comparative genomics pipeline

  Perl

  •

  MIT License

  •5•8•2•0•Updated May 20, 2024May 20, 2024