Purdue University

Trinity assembles transcript sequences from Illumina RNA-Seq data.

Trinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms.

Trnascan-se is a convenient, ready-for-use means to identify tRNA genes in one or more query sequences.

TRTools includes a variety of utilities for filtering, quality control and analysis of tandem repeats downstream of genotyping them from next-generation sequencing.

Trycycler is a tool for generating consensus long-read assemblies for bacterial genomes. I.e. if you have multiple long-read assemblies for the same isolate, Trycycler can combine them into a single assembly that is better than any of your inputs.

UCSC Executables is a variety of executables that perform functions ranging from sequence analysis and format conversion, to basic number crunching and statistics, to complex database generation and manipulation.

A communication library implementing high-performance messaging for MPI/PGAS frameworks.

Automated units conversion.

Automated units conversion.

Umi_tools is a collection of tools for handling Unique Molecular Identifiers in NGS data sets.

Unicycler is an assembly pipeline for bacterial genomes.

Usefulaf is an all-in-one Docker/Singularity image for single-cell processing with Alevin-fry(paper). It includes the all tools you need to turn your FASTQ files into a count matrix and then load it into your favorite analysis environment.

VADR is a suite of tools for classifying and analyzing sequences homologous to a set of reference models of viral genomes or gene families. It has been mainly tested for analysis of Norovirus, Dengue, and SARS-CoV-2 virus sequences in preparation for submission to the GenBank database.

An instrumentation framework for building dynamic analysis.

VarDictJava is a variant discovery program written in Java and Perl. It is a Java port of VarDict variant caller.

Variation graphs (vg) provides tools for working with genome variation graphs.

Varlociraptor implements a novel, unified fully uncertainty-aware approach to genomic variant calling in arbitrary scenarios.

Varscan is a tool used for variant detection in massively parallel sequencing data.

Vartrix is a software tool for extracting single cell variant information from 10x Genomics single cell data.

VAtools is a python package that includes several tools to annotate VCF files with data from other tools.