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•2•Updated Nov 11, 2024Nov 11, 2024

• Fungi_5k

  Public
  Fungi5k dataset analysis

  Python

  •0•0•0•0•Updated Nov 8, 2024Nov 8, 2024

• Compgenomics_Ecrusticola

  Public
  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

• stajichlab.github.io

  Public
  Stajich Lab Website

  genomefungimycology

  HTML

  •

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

  •313•0•0•0•Updated Oct 22, 2024Oct 22, 2024

• PopGenomics_Afumigatus_CEA10

  Public
  Explore CEA10 Strain variation

  R

  •

  MIT License

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

• PopGenomics_template

  Public template
  Template for Population Genomics variant calling

  R

  •

  MIT License

  •2•2•2•0•Updated Oct 17, 2024Oct 17, 2024

• PopGenomics_Afumigatus_Global

  Public
  A. fumigatus population genomics 2021 relaunch

  HTML

  •

  MIT License

  •0•0•0•0•Updated Oct 16, 2024Oct 16, 2024

• PopGenomics_Rhodotorula_mucilaginosa_NRRLY2510

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

  R

  •

  MIT License

  •0•0•0•0•Updated Sep 26, 2024Sep 26, 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

• SOP_data

  Public
  Standard Operating Procedures

  MIT License

  •0•0•5•0•Updated Sep 3, 2024Sep 3, 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

• 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 Aug 23, 2024Aug 23, 2024

• TaniaK_CF_Exophiala_dermatitidis

  Public
  Archiving repo from paper.

  HTML

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

• 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 Aug 7, 2024Aug 7, 2024

• stajichlab.github.io-v2

  Public archive
  lab site test

  HTML

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

• RolshausenLab_Aspergillus_DatePalm

  Public
  Aspergillus tubingensis DFA genome sequencing and annotation

  HTML

  •

  MIT License

  •1•1•0•0•Updated Jul 22, 2024Jul 22, 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

• PopGenomics_Cimmitis

  Public
  Population Genomics and CNV analysis of C. immitis strains

  HTML

  •

  MIT License

  •0•0•0•0•Updated Jun 25, 2024Jun 25, 2024

• Comparative_pipeline

  Public
  Comparative genomics pipeline

  Perl

  •

  MIT License

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

• Botrytis_sRNA_profile

  Public
  Re-processing public sRNA data from Botrytis

  R

  •

  MIT License

  •0•0•0•0•Updated Feb 25, 2024Feb 25, 2024

• Yugueros_cellwall_fungiphylogeny

  Public
  Phylogenomic analysis for cell wall composition profiling

  Shell

  •0•1•0•0•Updated Feb 22, 2024Feb 22, 2024

• PopGenomics_Bd

  Public
  Batrachochytrium dendrobatidis run

  Shell

  •

  MIT License

  •0•0•0•0•Updated Feb 15, 2024Feb 15, 2024

• make_simulated_genome

  Public
  Python

  •1•0•0•0•Updated Feb 6, 2024Feb 6, 2024

• find_ping_pong_JinfengPipeline

  Public
  Python

  •2•0•0•0•Updated Feb 6, 2024Feb 6, 2024