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Contents of README:Unipro UGENE is a multiplatform open-source software with the main goal of assisting molecular biologists without much expertise in bioinformatics to manage, analyze and visualize their data. UGENE integrates widely used bioinformatics tools within a common user interface. The toolkit supports multiple biological data formats and allows the retrieval of data from remote data sources. It provides visualization modules for biological objects such as: - annotated genome sequences - Next Generation Sequencing (NGS) assembly data - multiple sequence alignments - phylogenetic trees - 3D structures Most of the integrated algorithms are tuned for maximum performance by the usage of multithreading and special processor instructions. UGENE includes a visual environment for creating reusable workflows that can be launched on local resources or in a High Performance Computing (HPC) environment. UGENE is written in C++ using the Qt framework. The built-in plugin system and structured UGENE API make it possible to extend the toolkit with new functionality. EXTERNAL TOOLS UGENE can use and drive a number of external tools, providing a nice and unified GUI. These are not needed at build time, but are highly recommended for the complete (and extended) functionality of the program. Almost all of them can be found at SlackBuilds.org: - bedtools (A powerful toolset for genome arithmetic) - bowtie (A short read aligner of DNA sequences) - bowtie2 (A tool for aligning sequencing reads) - bwa (Burrows-Wheeler Aligner) - cap3 (CAP3: A DNA sequence assembly program) - cistrome-CEAS (CEAS: Cis-regulatory Element Annotation System) - cistrome-MACS (MACS: Model-based Analysis of ChIP-Seq) - clustalo (Clustal Omega) - clustalw (Multiple Sequence Alignment) - cufflinks (A reference-guided assembler for RNA-Seq experiments) - cutadapt (Trim adapters from high-throughput sequencing reads) - fastqc (A quality control tool for high throughput sequence data) - ncbi-blast (BLAST: Basic Local Alignment Search Tool) - ncbi-blast-plus (BLAST+ Command Line Applications) - PhyML (Phylogenetic estimation using Maximum Likelihood) - samtools (Sequence Alignment/Map Tools) - snpEff (Genetic variant annotation and effect prediction toolbox) - spades (SPAdes Genome Assembler) - spidey (mRNA-to-genomic alignment) - t_coffee (A multiple sequence alignment program) - tabix (Generic indexer for TAB-delimited genome position files ) - tophat (Splice junction mapper for RNA-Seq reads) - vcftools (A program package designed for working with VCF files) Alternatively, check the program's website if you want to get them precompiled. CITING: Unipro UGENE: a unified bioinformatics toolkit Konstantin Okonechnikov; Olga Golosova; Mikhail Fursov; the UGENE team Bioinformatics 2012 28: 1166-1167 |
Name Last modified Size
Parent Directory - README 29-Mar-2015 01:44 2.7K References 14-Dec-2013 18:05 194 doinst.sh 26-Nov-2013 10:57 129 slack-desc 20-Jun-2015 07:01 1.0K ugene.SlackBuild 20-Jun-2015 07:01 3.1K ugene.info 20-Jun-2015 07:01 355
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