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    24 repositories

    • CTAT-LR-fusion

      Public
      fusion transcript detection using long reads, leveraging ctat-minimap2 and FusionInspector
      Perl
      •
      Other
      •0•14•5•0•Updated Dec 18, 2024Dec 18, 2024

    • ctat-minimap2

      Public
      A versatile pairwise aligner for genomic and spliced nucleotide sequences
      C
      •
      Other
      •424•1•0•0•Updated Dec 18, 2024Dec 18, 2024

    • rnaseqc

      Public
      Fast, efficient RNA-Seq metrics for quality control and process optimization
      C++
      •
      Other
      •19•0•0•0•Updated Nov 26, 2024Nov 26, 2024

    • CTAT-SPLICING

      Public
      detection of cancer splicing aberrations
      Perl
      •
      Other
      •3•8•6•0•Updated Nov 22, 2024Nov 22, 2024

    • ctat-mutations-benchmarking

      Public
      benchmarking utilities for ctat-mutations
      Python
      •0•1•0•0•Updated Oct 29, 2024Oct 29, 2024

    • ctat-mutations

      Public
      Mutation detection using GATK4 best practices and latest RNA editing filters resources. Works with both Hg38 and Hg19
      HTML
      •
      Other
      •18•74•44•0•Updated Jul 20, 2024Jul 20, 2024

    • CTAT_VIF_Paper

      Public
      Python
      •0•0•0•0•Updated Jun 24, 2024Jun 24, 2024

    • CTAT-VirusIntegrationFinder

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •5•15•3•1•Updated Nov 22, 2023Nov 22, 2023

    • ctat-genome-lib-builder

      Public
      Software used by Trinity CTAT for building CTAT Genome Libs, resource databases shared by Trinity CTAT components
      Perl
      •
      BSD 3-Clause "New" or "Revised" License
      •2•10•10•1•Updated Oct 27, 2023Oct 27, 2023

    • Trinity_CTAT

      Public
      34•116•3•1•Updated Sep 5, 2023Sep 5, 2023

    • CTAT-pVACseq

      Public
      WDL
      •1•1•0•0•Updated Jul 7, 2023Jul 7, 2023

    • BatVI

      Public
      WDL and docker image for running BatVI
      WDL
      •
      MIT License
      •1•0•0•0•Updated Dec 22, 2022Dec 22, 2022

    • VirusFinder2_VERSE

      Public
      A copy of VirusFinder2/VERSE, used for identifying viral integrations.
      C
      •
      MIT License
      •3•0•0•0•Updated Apr 6, 2022Apr 6, 2022

    • ViFi

      Public
      Pipeline for identifying viral integration and fusion mRNA reads from NGS data. Manuscript is currently in preparation.
      Python
      •
      GNU General Public License v3.0
      •18•0•0•0•Updated Mar 18, 2022Mar 18, 2022

    • ctat-mutations-pVACseq

      Public
      0•2•0•0•Updated Mar 7, 2022Mar 7, 2022

    • ctat_mutation_ext_testdata

      Public
      extended testing data for ctat mutations pipe
      0•1•0•0•Updated Aug 26, 2021Aug 26, 2021

    • arcasHLA

      Public
      Fast and accurate in silico inference of HLA genotypes from RNA-seq
      Python
      •
      GNU General Public License v3.0
      •51•0•0•0•Updated Apr 14, 2021Apr 14, 2021

    • RnaVariantBenchmarking

      Public
      code for running alternative rna-based variant detection tools and benchmarking
      Python
      •2•0•0•0•Updated May 18, 2020May 18, 2020

    • bamsurgeon

      Public
      tools for adding mutations to existing .bam files, used for testing mutation callers
      Python
      •
      MIT License
      •86•0•0•0•Updated Jun 14, 2019Jun 14, 2019

    • ctat-centrifuge

      Public
      find viruses and microbes using centrifuge
      Perl
      •0•0•0•0•Updated Apr 19, 2019Apr 19, 2019

    • mutations

      Public
      calling variants from RNA-Seq data
      Python
      •1•4•0•0•Updated Nov 10, 2017Nov 10, 2017

    • GenomeGuidedTransRecon

      Public
      Genome guided transcript reconstruction
      0•0•0•0•Updated Oct 24, 2017Oct 24, 2017

    • expression

      Public
      transcript expression quantification
      0•0•0•0•Updated Oct 24, 2017Oct 24, 2017

    • lncRNA

      Public
      lncRNA classification
      0•0•0•0•Updated Oct 24, 2017Oct 24, 2017