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

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.

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

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

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.

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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HTSlib is a C library used for reading and writing high-throughput sequencing data.

Relion (REgularised LIkelihood OptimisatioN) is a stand-alone computer program for the refinement of 3D reconstructions or 2D class averages in electron cryo-microscopy. 

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