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Owens

Perl is a family of programming languages.

Owens

StringTie assembles aligned RNA-Seq reads into transcripts that represent splice variants in RNA-Seq samples.

Oakley, Owens

Cufflinks is a program that analyzes RNA -Seq samples. It assembles aligned RNA-Seq reads into a set of transcripts, then inspects the transcripts to estimate abundances and test for differential expression and regulation in the RNA-Seq reads.

Owens

HISAT2 is a graph-based alignment program that maps DNA and RNA sequencing reads to a population of human genomes.

Oakley, Owens

TopHat uses Bowtie, a high-throughput short read aligner, to analyze the mapping results for RNA-Seq reads and identify splice junctions.

 

Please note that tophat (and bowtie) cannot run in parallel, that is, on multiple nodes.  Submitting multi-node jobs will only waste resources.  In addition you must explicitly include the '-p' option to use multiple threads on a single node.

Owens

TAU Commander is a user interface for the TAU Performance System, a set of tools for analyizing the performance of parallel programs. 

Owens

Salmon is a tool for quantifying the expression of transcripts using RNA-seq data.

Owens

Kallisto is an RNA-seq quantification program. It quantifies abundances of transcripts from RNA-seq data and uses psedoalignment to determine the compatibility of reads with targets, without needing alignment.

Owens

Singularity is a container system designed for use on High Performance Computing (HPC) systems. It allows users to run both Docker and Singularity containers.

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