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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 9 4

  2. AAFTF AAFTF Public

    Automatic Assembly For The Fungi

    Python 20 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 209 repositories
  • Fungi_5k Public

    Fungi5k dataset analysis

    stajichlab/Fungi_5k’s past year of commit activity
    Python 0 1 0 0 Updated Apr 24, 2025
  • PopGenomics_Cimmitis Public

    Population Genomics and CNV analysis of C. immitis strains

    stajichlab/PopGenomics_Cimmitis’s past year of commit activity
    HTML 0 MIT 0 0 0 Updated Apr 23, 2025
  • PopGenomics_Cposadasii Public

    C.posa variant calling and CNV exploration using

    stajichlab/PopGenomics_Cposadasii’s past year of commit activity
    Shell 0 MIT 0 0 0 Updated Apr 23, 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 Apr 18, 2025
  • DhingraLab_Afum_ncRNA Public

    A. fumigatus Temp and delta-ncRNA analysis

    stajichlab/DhingraLab_Afum_ncRNA’s past year of commit activity
    R 0 0 0 0 Updated Apr 16, 2025
  • stajichlab.github.io Public Forked from greenelab/lab-website-template

    Stajich Lab Website

    stajichlab/stajichlab.github.io’s past year of commit activity
    HTML 0 BSD-3-Clause 354 0 0 Updated Apr 16, 2025
  • 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 9 MIT 4 7 1 Updated Apr 14, 2025
  • Afumigatus_RefStrains Public

    Reference A. fumigatus strain panel

    stajichlab/Afumigatus_RefStrains’s past year of commit activity
    Shell 1 0 0 0 Updated Apr 11, 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
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