The table below lists some of the Open-Source applications installed and available on the Bari-ReCaS Data-Center.

On request, additional Open-Source products can be installed and made available. For commercial products,  a bit more investigation is required.

If you need an Open-Source product non listed here or a commercial one please contact the ReCaS team.

Scientific Area

Software

Description

BIOINFORMATICS

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.

ABySS 

 

ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads. The single-processor version is useful for assembling genomes up to 100 Mbases in size. The parallel version is implemented using MPI and is capable of assembling larger genomes.

BEAST

BEAST is a cross-platform program for Bayesian analysis of molecular sequences using MCMC. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology.

Mothur

Mothur aims to be a comprehensive software package that allows users to use a single piece of software to analyze community sequence data. It builds upon previous tools to provide a flexible and powerful software package for analyzing sequencing data.

SOAPdenovo

SOAPdenovo2-src-r240 is a novel short-read assembly method that can build a de novo draft assembly for human-sized genomes. The program is specially designed to assemble Illumina short reads. It creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost effective way.

Velvet

Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454. Velvet currently takes in short read sequences, removes errors then produces high quality unique contigs. It then uses paired-end read and long read information, when available, to retrieve the repeated areas between contigs.

Velvet Optimizer

Velvet Optimizer is a multi-threaded Perl script for automatically optimising the three primary parameter options (K, -exp_cov, -cov_cutoff) for the Velvet de novo sequence assembler.

SPAdes

SPAdes – St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. The current version of SPAdes works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads.

BWA

 

BWA is a program for aligning sequencing reads against a large reference genome (e.g. human genome). It has two major components, one for read shorter than 150bp and the other for longer reads.

Trinity

Trinity 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.

AmpliconNoise

 

AmpliconNoise is a collection of programs for the removal of noise from 454 sequenced PCR amplicons. It involves two steps the removal of noise from the sequencing itself and the removal of PCR point errors.

MrBayes

MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. MrBayes uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters.

GSNAP

 

GSNAP (Genomic Short-read Nucleotide Alignment Program) can align both single-end and paired-end reads as short as 14 nt and of arbitrarily long length. It can detect short- and long-distance splicing, including interchromosomal splicing, in individual reads using probabilistic models or a database of known splice sites.
SCARPA Scarpa is a stand-alone scaffolding tool for NGS data. It can be used together with virtually any genome assembler and any NGS read mapper that supports SAM format. Scarpa is available free of charge for academic and commercial use under the GNU General Public License (GPL).
G-NEST Gene Neighborhood Scoring Tool (G-NEST) combines genomic location, gene expression, and evolutionary sequence conservation data to score putative gene neighborhoods across all possible window sizes simultaneously.
TopHat 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.
PLINK Plink is a free, commonly used, open-source whole genome association analysis toolset designed by Shaun Purcell. The software is designed flexibly to perform a wide range of basic, large-scale genetic analyses.
DETONATE DETONATE (DE novo TranscriptOme rNa-seq Assembly with or without the Truth Evaluation) consists of two component packages, RSEM-EVAL and REF-EVAL. Both packages are mainly intended to be used to evaluate de novo transcriptome assemblies, although REF-EVAL can be used to compare sets of any kinds of genomic sequences.
fcGENE fcGENE is a free, open-source Format Converting tool for genotype SNP data. Its main purpose is to simplify the process of imputation-based Genome wide association studies(GWAS).
HTSeq HTSeq is a Python package that provides infrastructure to process data from high-throughput sequencing assays.

STATISTICAL

R

R is a free software environment for statistical computing and graphics.

ROOT Cern

ROOT Cern is a modular scientific software framework. It provides all the functionalities needed to deal with big data processing, statistical analysis, visualisation and storage.

NEUROIMAGING PROCESSING

FSL

 FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.

FreeSurfer

FreeSurfer is an open source software suite for processing and analyzing (human) brain MRI images.

MRIcron

MRIcron is a cross-platform NIfTI format image viewer. It can load multiple layers of images, generate volume renderings and draw volumes of interest. It also provides dcm2nii for converting DICOM images to NIfTI format and NPM for statistics.