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diff --git a/academic/ugene/README b/academic/ugene/README index 713391c36cb4f..4d1fc9662bb38 100644 --- a/academic/ugene/README +++ b/academic/ugene/README @@ -7,11 +7,11 @@ 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. +- 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 @@ -21,20 +21,34 @@ be launched on local resources or in a High Performance Computing built-in plugin system and structured UGENE API make it possible to extend the toolkit with new functionality. -CITING: -If you use UGENE in your work, please quote this publication: -Unipro UGENE: a unified bioinformatics toolkit -Konstantin Okonechnikov, Olga Golosova, Mikhail Fursov, the UGENE team -Bioinformatics 2012 28: 1166-1167 doi: 10.1093/bioinformatics/bts091 +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) -NOTE! -While not needed for building of UGENE, the dependencies listed as -"REQUIRED" are highly recommended for the complete functionality of -the program. UGENE will also drive spidey if you have it installed, -but keep in mind that it is available only as a 32-bit binary. +Alternatively, check the program's website if you want to get them +precompiled. -NOTE ABOUT CUDA: -UGENE is built without CUDA support and CUDA-BLAST is not included -among the "REQUIRED", either. Simply, I do not have the hardware. If -someone is interested in such functionality and can offer help with -the script, please contact me. +CITING: +Unipro UGENE: a unified bioinformatics toolkit +Konstantin Okonechnikov; Olga Golosova; Mikhail Fursov; the UGENE team +Bioinformatics 2012 28: 1166-1167 |