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35538e5091
Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org> |
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ugene.info | ||
ugene.SlackBuild |
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. IMPORTANT: 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: - cistrome-CEAS (CEAS: Cis-regulatory Element Annotation System) - cistrome-MACS (MACS: Model-based Analysis of ChIP-Seq) - cufflinks (A reference-guided assembler for RNA-Seq experiments) - 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) - clustalo (Clustal Omega) - clustalw (Multiple Sequence Alignment) - ncbi-blast (BLAST: Basic Local Alignment Search Tool) - ncbi-blast-plus (BLAST+ Command Line Applications) - samtools (Sequence Alignment/Map Tools) - 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