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@stajichlab

Jason Stajich Lab at UC Riverside

Evolutionary Genomics of Fungi projects, data and software
README.md

These repositories for the Stajich laboratory at UC Riverside focused on Genomics, Bioinformatics, Evolution of (mostly) Fungi and Microbes.

https://lab.stajich.org

See our Standard Operating Procedures are (in progress) documentation on procedures and onboarding.

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  1. PHYling 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)

    Python 8 3

  2. AAFTF AAFTF Public

    Automatic Assembly For The Fungi

    Python 19 4

  3. SOP_data SOP_data Public

    Standard Operating Procedures

  4. funannotate_template funannotate_template Public template

    Project template for doing a funannotate annotation set

    Shell 1 1

  5. PopGenomics_template PopGenomics_template Public template

    Template for Population Genomics variant calling

    Shell 2 2

  6. Comparative_pipeline Comparative_pipeline Public

    Comparative genomics pipeline

    Perl 9 6

Repositories

Showing 10 of 210 repositories
  • 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)

    stajichlab/PHYling’s past year of commit activity
    Python 8 MIT 3 6 0 Updated Mar 12, 2025
  • ExtremeRhodotorula_Hybrid_Diploid Public

    Investigating potential diploid/hybrid strains

    stajichlab/ExtremeRhodotorula_Hybrid_Diploid’s past year of commit activity
    Python 0 0 0 0 Updated Mar 3, 2025
  • RHIEPA_Sordariomycetes_orthologs Public

    OrthoFinder results for use in RHIEPA analysis for Sordariomycetes

    stajichlab/RHIEPA_Sordariomycetes_orthologs’s past year of commit activity
    Shell 0 0 0 0 Updated Feb 21, 2025
  • CramerLab_Afumigatus_AF293_VOR Public Forked from stajichlab/PopGenomics_Afumigatus_CEA10

    Explore AF293 VOR Strain Evolution

    stajichlab/CramerLab_Afumigatus_AF293_VOR’s past year of commit activity
    R 0 MIT 1 0 0 Updated Feb 18, 2025
  • PopGenomics_Afumigatus_CEA10 Public

    Explore CEA10 Strain variation

    stajichlab/PopGenomics_Afumigatus_CEA10’s past year of commit activity
    R 0 MIT 1 0 0 Updated Feb 18, 2025
  • Compgenomics_Ecrusticola Public

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

    stajichlab/Compgenomics_Ecrusticola’s past year of commit activity
    Python 1 0 0 0 Updated Feb 13, 2025
  • RolshausenLab_Aspergillus_DatePalm Public

    Aspergillus tubingensis DFA genome sequencing and annotation

    stajichlab/RolshausenLab_Aspergillus_DatePalm’s past year of commit activity
    Shell 1 MIT 1 0 0 Updated Feb 12, 2025
  • Fungi_5k Public

    Fungi5k dataset analysis

    stajichlab/Fungi_5k’s past year of commit activity
    Python 0 1 0 0 Updated Feb 11, 2025
  • DhingraLab_Afum_ncRNA Public

    A.fumigatus ncRNA analysis

    stajichlab/DhingraLab_Afum_ncRNA’s past year of commit activity
    Shell 0 0 0 0 Updated Feb 6, 2025
  • ExtremeRhodotorula_RefGenomes Public

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

    stajichlab/ExtremeRhodotorula_RefGenomes’s past year of commit activity
    Shell 0 MIT 0 0 0 Updated Feb 5, 2025
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