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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

    R 2 2

  6. Comparative_pipeline Comparative_pipeline Public

    Comparative genomics pipeline

    Perl 8 5

Repositories

Showing 10 of 206 repositories
  • Compgenomics_Ecrusticola Public
    stajichlab/Compgenomics_Ecrusticola’s past year of commit activity
    Python 0 0 0 0 Updated Oct 18, 2024
  • PopGenomics_Afumigatus_CEA10 Public

    Explore CEA10 Strain variation

    stajichlab/PopGenomics_Afumigatus_CEA10’s past year of commit activity
    R 0 MIT 0 0 0 Updated Oct 17, 2024
  • PopGenomics_template Public template

    Template for Population Genomics variant calling

    stajichlab/PopGenomics_template’s past year of commit activity
    R 2 MIT 2 2 0 Updated Oct 16, 2024
  • 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 Oct 16, 2024
  • PopGenomics_Rhodotorula_mucilaginosa_NRRLY2510 Public

    Rhodotorula mucilaginosa population genomics with ref strain NRRL Y-2510

    stajichlab/PopGenomics_Rhodotorula_mucilaginosa_NRRLY2510’s past year of commit activity
    R 0 MIT 0 0 0 Updated Sep 26, 2024
  • Fungi_5k Public

    Fungi5k dataset analysis

    stajichlab/Fungi_5k’s past year of commit activity
    Shell 0 0 0 0 Updated Sep 26, 2024
  • Acarospora_socialis_annotation Public

    Annotation of Acarospora socialis genome for CCGP

    stajichlab/Acarospora_socialis_annotation’s past year of commit activity
    Shell 0 0 0 0 Updated Sep 25, 2024
  • funannotate_template Public template

    Project template for doing a funannotate annotation set

    stajichlab/funannotate_template’s past year of commit activity
    Shell 1 MIT 1 0 0 Updated Sep 25, 2024
  • 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 Sep 24, 2024
  • ExtremeRhodotorula_DraftGenomes Public

    Draft genomes from short read data

    stajichlab/ExtremeRhodotorula_DraftGenomes’s past year of commit activity
    Shell 0 MIT 0 0 0 Updated Sep 19, 2024
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