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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 7 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 8 5

Repositories

Showing 10 of 207 repositories
  • PopGenomics_template Public template

    Template for Population Genomics variant calling

    stajichlab/PopGenomics_template’s past year of commit activity
    Shell 2 MIT 2 2 0 Updated Jan 28, 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 7 MIT 3 6 1 Updated Jan 27, 2025
  • AAFTF Public

    Automatic Assembly For The Fungi

    stajichlab/AAFTF’s past year of commit activity
    Python 19 MIT 4 10 0 Updated Jan 23, 2025
  • Fungi_5k Public

    Fungi5k dataset analysis

    stajichlab/Fungi_5k’s past year of commit activity
    Python 0 0 0 0 Updated Jan 23, 2025
  • PopGenomics_Afumigatus_Global Public

    A. fumigatus population genomics 2021 relaunch

    stajichlab/PopGenomics_Afumigatus_Global’s past year of commit activity
    HTML 0 MIT 0 0 0 Updated Jan 22, 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 325 0 0 Updated Jan 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.

    stajichlab/moss_mycobiome’s past year of commit activity
    HTML 0 0 0 0 Updated Jan 15, 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 Jan 10, 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 Dec 29, 2024
  • MATPredict Public

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

    stajichlab/MATPredict’s past year of commit activity
    Python 0 0 0 0 Updated Dec 17, 2024
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