Life Sciences

BOWTIE

Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end).

Usage

List available versions

module avail bowtie
module load bowtie
module show bowtie

GATE

GATE is an advanced opensource software developed by the international OpenGATE collaboration and dedicated to numerical simulations in medical imaging and radiotherapy. It currently supports simulations of Emission Tomography (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), Computed Tomography (CT), Optical Imaging (Bioluminescence and Fluorescence) and Radiotherapy experiments. Using an easy-to-learn macro mechanism to configurate simple or highly sophisticated experimental settings, GATE now plays a key role in the design of new medical imaging devices, in the optimization of acquisition protocols and in the development and assessment of image reconstruction algorithms and correction techniques. It can also be used for dose calculation in radiotherapy experiments.

List available versions

module avail gate

PASHA

http://pasha.sourceforge.net/homepage.htm#latest

PASHA is a parallel short read assembler for large genomes using de Bruijn graphs. Taking advantage of both shared-memory multi-core CPUs and distributed-memory compute clusters, PASHA has demonstrated its potential to perform high-quality de-novo assembly of large genomes in reasonable time with modest computing resources. Our evaluation using three small real paired-end datasets shows that PASHA is able to produce better assemblies with comparable genome coverage and mis-assembly rates compared to three leading assemblers: Velvet, ABySS and SOAPdenovo. Moreover, PASHA achieves the fastest speed for all three datasets on a single CPU. For the human genome, PASHA achieves competitive assembly quality with ABySS and is able to complete the assembly in about 21 hours, which is about 2.38 times faster than ABySS on the same hardware configurations.

List available versions

module avail pasha

Ray

http://denovoassembler.sourceforge.net/

Ray is a parallel software that computes de novo genome assemblies with next-generation sequencing data.

Ray is written in C++ and can run in parallel on numerous interconnected computers using the message-passing interface (MPI) standard.

Ray is maintained by Sébastien Boisvert, a PhD student supervised by Jacques Corbeil and François Laviolette at Université Laval, in Québec, Canada.

List available versions

module avail ray

Tophat

https://ccb.jhu.edu/software/tophat/index.shtml

TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.

TopHat is a collaborative effort among Daehwan Kim and Steven Salzberg in the Center for Computational Biology at Johns Hopkins University, and Cole Trapnell in the Genome Sciences Department at the University of Washington. TopHat was originally developed by Cole Trapnell at the Center for Bioinformatics and Computational Biology at the University of Maryland, College Park.

List available versions

module avail tophat

Trinity

https://github.com/trinityrnaseq/trinityrnaseq/wiki

Trinity, developed at the Broad Institute and the Hebrew University of Jerusalem, represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-seq reads. Trinity partitions the sequence data into many individual de Bruijn graphs, each representing the transcriptional complexity at a given gene or locus, and then processes each graph independently to extract full-length splicing isoforms and to tease apart transcripts derived from paralogous genes.

List available versions

module avail trinity