Pinned Repositories
Trinity_CTAT
ctat-mutations
Mutation detection using GATK4 best practices and latest RNA editing filters resources. Works with both Hg38 and Hg19
ctat-genome-lib-builder
Software used by Trinity CTAT for building CTAT Genome Libs, resource databases shared by Trinity CTAT components
CTAT-VirusIntegrationFinder
CTAT-LR-fusion
fusion transcript detection using long reads, leveraging ctat-minimap2 and FusionInspector
mutations
calling variants from RNA-Seq data
ctat-mutations-pVACseq
ctat-minimap2
A versatile pairwise aligner for genomic and spliced nucleotide sequences
ctat-mutations-benchmarking
benchmarking utilities for ctat-mutations
ctat_mutation_ext_testdata
extended testing data for ctat mutations pipe
TrinityCTAT's Repositories
TrinityCTAT/ctat-mutations
Mutation detection using GATK4 best practices and latest RNA editing filters resources. Works with both Hg38 and Hg19
TrinityCTAT/CTAT-LR-fusion
fusion transcript detection using long reads, leveraging ctat-minimap2 and FusionInspector
TrinityCTAT/CTAT_VIF_Paper
TrinityCTAT/ctat-mutations-benchmarking
benchmarking utilities for ctat-mutations
TrinityCTAT/CTAT-VirusIntegrationFinder
TrinityCTAT/ctat-genome-lib-builder
Software used by Trinity CTAT for building CTAT Genome Libs, resource databases shared by Trinity CTAT components
TrinityCTAT/Trinity_CTAT
TrinityCTAT/ctat-minimap2
A versatile pairwise aligner for genomic and spliced nucleotide sequences
TrinityCTAT/rnaseqc
Fast, efficient RNA-Seq metrics for quality control and process optimization
TrinityCTAT/BatVI
WDL and docker image for running BatVI
TrinityCTAT/VirusFinder2_VERSE
A copy of VirusFinder2/VERSE, used for identifying viral integrations.
TrinityCTAT/ViFi
Pipeline for identifying viral integration and fusion mRNA reads from NGS data. Manuscript is currently in preparation.
TrinityCTAT/ctat-mutations-pVACseq
TrinityCTAT/ctat_mutation_ext_testdata
extended testing data for ctat mutations pipe
TrinityCTAT/arcasHLA
Fast and accurate in silico inference of HLA genotypes from RNA-seq
TrinityCTAT/RnaVariantBenchmarking
code for running alternative rna-based variant detection tools and benchmarking
TrinityCTAT/bamsurgeon
tools for adding mutations to existing .bam files, used for testing mutation callers
TrinityCTAT/ctat-centrifuge
find viruses and microbes using centrifuge
TrinityCTAT/mutations
calling variants from RNA-Seq data
TrinityCTAT/GenomeGuidedTransRecon
Genome guided transcript reconstruction
TrinityCTAT/expression
transcript expression quantification
TrinityCTAT/lncRNA
lncRNA classification