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70 lines
3.3 KiB
Text
70 lines
3.3 KiB
Text
Unipro UGENE is a multiplatform open-source software with the main
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goal of assisting molecular biologists without much expertise in
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bioinformatics to manage, analyze and visualize their data.
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UGENE integrates widely used bioinformatics tools within a common user
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interface. The toolkit supports multiple biological data formats and
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allows the retrieval of data from remote data sources. It provides
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visualization modules for biological objects such as:
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- annotated genome sequences
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- Next Generation Sequencing (NGS) assembly data
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- multiple sequence alignments
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- phylogenetic trees
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- 3D structures
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Most of the integrated algorithms are tuned for maximum performance by
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the usage of multithreading and special processor instructions. UGENE
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includes a visual environment for creating reusable workflows that can
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be launched on local resources or in a High Performance Computing
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(HPC) environment. UGENE is written in C++ using the Qt framework. The
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built-in plugin system and structured UGENE API make it possible to
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extend the toolkit with new functionality.
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CITING:
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Unipro UGENE: a unified bioinformatics toolkit
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Konstantin Okonechnikov; Olga Golosova; Mikhail Fursov; the UGENE team
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Bioinformatics 2012 28: 1166-1167
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EXTERNAL TOOLS
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UGENE can use and drive a number of external tools, providing a nice
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and unified GUI. These are not needed at build time, but are highly
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recommended for the complete (and extended) functionality of the
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program. All of them are available at SlackBuilds.org:
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- bedGraphToBigWig (Convert bedGraph to bigWig file)
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- bedtools (A powerful toolset for genome arithmetic)
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- bowtie (A short read aligner of DNA sequences)
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- bowtie2 (A tool for aligning sequencing reads)
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- bwa (Burrows-Wheeler Aligner)
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- cap3 (CAP3: A DNA sequence assembly program)
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- cistrome-CEAS (CEAS: Cis-regulatory Element Annotation System)
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- cistrome-conductGO (Find the top-n highest expressed TFs)
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- cistrome-extra (Cistrome Applications Harvard extra apps)
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- cistrome-MACS (MACS: Model-based Analysis of ChIP-Seq)
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- cistrome-mdseqpos (Cistrome Applications Harvard mdseqpos)
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- clark-ugene (Ugene's forked CLAssifier based on Reduced K-mers)
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- clustalo (Clustal Omega)
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- clustalw (Multiple Sequence Alignment)
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- cufflinks (A reference-guided assembler for RNA-Seq experiments)
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- cutadapt (Trim adapters from high-throughput sequencing reads)
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- diamond (A sequence aligner for protein and translated DNA)
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- fastqc (A quality control tool for high throughput sequence data)
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- HMMER (Biosequence analysis using profile hidden Markov models)
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- kraken (Assign taxonomic labels to short DNA sequences)
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- MetaPhlAn (Metagenomic Phylogenetic Analysis)
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- ncbi-blast (BLAST: Basic Local Alignment Search Tool)
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- ncbi-blast+ (BLAST+ Command Line Applications)
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- PhyML (Phylogenetic estimation using Maximum Likelihood)
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- samtools-legacy (Sequence Alignment/Map Tools)
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- snpEff (Genetic variant annotation and effect prediction toolbox)
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- spades (SPAdes Genome Assembler)
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- spidey (mRNA-to-genomic alignment)
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- t_coffee (A multiple sequence alignment program)
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- tabix-legacy (Generic indexer for TAB-delimited genome position files )
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- tophat (Splice junction mapper for RNA-Seq reads)
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- trimmomatic (A flexible read trimming tool for Illumina NGS data)
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- vcftools (A program package designed for working with VCF files)
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Alternatively, check the program's website if you want to get them
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precompiled.
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