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arcashla

Fast and accurate in silico inference of HLA genotypes from RNA-seq

bamsurgeon

tools for adding mutations to existing .bam files, used for testing mutation callers

batvi

WDL and docker image for running BatVI

ctat-centrifuge

find viruses and microbes using centrifuge

ctat-genome-lib-builder

Software used by Trinity CTAT for building CTAT Genome Libs, resource databases shared by Trinity CTAT components

ctat-lr-fusion

fusion transcript detection using long reads, leveraging ctat-minimap2 and FusionInspector

ctat-minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences

ctat-mutations

Mutation detection using GATK4 best practices and latest RNA editing filters resources. Works with both Hg38 and Hg19

ctat-mutations-benchmarking

benchmarking utilities for ctat-mutations

ctat-mutations-pvacseq

ctat-pvacseq

ctat-splicing

detection of cancer splicing aberrations

ctat-virusintegrationfinder

ctat_mutation_ext_testdata

extended testing data for ctat mutations pipe

ctat_vif_paper

expression

transcript expression quantification

genomeguidedtransrecon

Genome guided transcript reconstruction

lncrna

lncRNA classification

mutations

calling variants from RNA-Seq data

rnaseqc

Fast, efficient RNA-Seq metrics for quality control and process optimization

rnavariantbenchmarking

code for running alternative rna-based variant detection tools and benchmarking

trinity_ctat

vifi

Pipeline for identifying viral integration and fusion mRNA reads from NGS data. Manuscript is currently in preparation.

virusfinder2_verse

A copy of VirusFinder2/VERSE, used for identifying viral integrations.