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39 followers · 488 following
  • University of California, Santa Cruz
  • Santa Cruz, CA
  • X @kokyriakidis

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Achievement: QuickdrawAchievement: Pull Sharkx2Achievement: YOLOAchievement: Arctic Code Vault Contributor

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  • shasta Public

    Forked from paoloshasta/shasta

    De novo assembly from Oxford Nanopore reads.

    C++ Other Updated Sep 21, 2024

  • cre Public

    Forked from naumenko-sa/cre

    excel report generation using data from bcbio variant2 germline pipeline

    Shell MIT License Updated Sep 13, 2024

  • bcbio-nextgen Public

    Forked from bcbio/bcbio-nextgen

    Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis

    Python MIT License Updated Aug 24, 2024

  • GFAse Public

    Forked from rlorigro/GFAse

    Tool for globally phasing diploid assembly graphs with orthogonal data

    C++ Mozilla Public License 2.0 Updated Aug 24, 2024

  • dna-seq-varlociraptor Public

    Forked from snakemake-workflows/dna-seq-varlociraptor

    A Snakemake workflow for calling small and structural variants under any kind of scenario (tumor/normal, tumor/normal/relapse, germline, pedigree, populations) via the unified statistical model of …

    Python MIT License Updated Aug 13, 2024

  • rnafusion Public

    Forked from nf-core/rnafusion

    RNA-seq analysis pipeline for detection gene-fusions

    Nextflow 1 MIT License Updated Aug 8, 2024

  • cloudbiolinux Public

    Forked from chapmanb/cloudbiolinux

    CloudBioLinux: configure virtual (or real) machines with tools for biological analyses

    Python MIT License Updated Dec 12, 2023

  • pfb2023 Public

    Forked from brianjohnhaas/pfb2023

    Programming for Biology @ CSHL 2023

    Python Updated Oct 22, 2023

  • pbRUGD-workflow Public

    Forked from amwenger/pbRUGD-workflow

    Workflow for the comprehensive detection and prioritization of variants in human genomes with PacBio HiFi reads

    Python BSD 3-Clause Clear License Updated Nov 22, 2021

  • precisionFDAsubmission Public

    GENeTres Submission scripts used in the Truth Challenge V2: Calling Variants from Short and Long Reads in Difficult-to-Map Regions

    Shell 2 Updated Jul 27, 2021

  • GSOC2020_RNASeq Public

    Selection test for the project named: "Creating a new pipeline for long-read RNA-seq using StringTie v2"

    Shell Updated Mar 4, 2020

  • bcbioSmallRna Public

    Forked from lpantano/bcbioSmallRna

    R package to analyze data after small RNAseq with bcbio

    HTML MIT License Updated Mar 1, 2020

  • batchtoolscc Public

    Extension Package for Batchtools. Fine-Tuned for Compute Canada HPC Systems

    R Updated Dec 4, 2019

  • RNASeq Public

    Pipeline for RNA-Seq PBS script submission in Cluster

    Java Updated Dec 29, 2018