{AnyApplication} 1.0.0 true full.tools.cistrome Cistrome External tools for the Cistrome workflow. 2.0.8 2016-02-02 true 56 tools.7z 586931ad2ec5df6d98cffc721cc3d918111f1aab full.tools.cutadapt Cutadapt Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. 1.7.1 2016-02-02 true 78 full.tools.python tools.7z 4a576618c6f915728d6997b4edb4a6ef0669a1d0 full.tools.perl Perl Perl is a highly capable, feature-rich programming language. 5.10.0.5 2013-06-24 true 68 tools.7z cd70c373dfc8f9e824dcaa615b7bf2f6bac76b9a full.tools.spidey Spidey Spidey is an mRNA-to-genomic alignment program. 1 2016-02-02 true 60 tools.7z 247c545f43b68682fbd8ccaff343634236bb4bd0 NGS.cistrome Data for the Cistrome workflow (for ChIP-Seq) Sample data for the Cistrome workflow. 1.0.0 2010-07-15 1 data.7z 7eadbe8215ac6a09a591443c89b23d47ad2ac97a full Full package additions Full package additions. 1.29.0 2017-12-29 90 true c3ad421b2968ee65c661b9f53aaeb2be5c4d5575 full.tools External tools External tools. 1.29.0 2017-12-29 90 true a75e4989a3031bf7aa06f10f9876ecdb2de80e99 ugene Standard package Standard package contains executables and data of Unipro UGENE. true true 1.29.0 2017-12-29 100 9ce3e1826bd3085aa7fc6b7a5bd964bbcf6d6e3d installer UGENE Maintenance Tool An installation and update tool for Unipro UGENE. true true true 3.0.3.1 2018-05-31 100 content.7z f259fa9342975e25a3b22010389e936d8de97571 ngs_classification.wevote.tools WEVOTE external tools Check this component to install WEVOTE executables. ngs_classification.taxonomy 1.0.0 2018-01-29 100 tools.7z 2ac3617b2eef014e7d5f5eed3cd8274bdeef3574 ngs_classification.refseq RefSeq reference data Check this component to download NCBI RefSeq bacterial, viral and human data. The data can be used to build a database for CLARK. To build a database for Kraken unpack the data first. 1.0.0 2018-08-06 90 c6b76007fa7088256e2844543f9d5a6c8a8501af NGS NGS additions: ChIP-Seq data analysis The component contains external tools and reference data, required to analyze ChIP-Seq data with the Cistrome workflow. 1.0.0 2016-02-02 80 3c91af0bbe9df613009cd9b883e7abb68828e0a6 ngs_classification NGS additions: metagenomics classification The component contains external tools and reference data for taxonomy classification of metagenomic whole-genome shotgun sequencing data. 1.0.0 2017-12-08 85 a4a34ed770d047aec294155680756a9a5242c946 ngs_classification.clark Classification with CLARK CLARK (CLAssifier based on Reduced K-mers) is a tool for taxonomy classification of metagenomic NGS data. Databases with viral and viral+bacterial NCBI RefSeq data are provided by default for CLARK-l variant of the tool launched with default parameters. One can also build a custom database. 1.31.0 2018-08-17 70 324fc963113967e9a671b2fcabfa8cb4c289a52d ngs_classification.diamond Classification with DIAMOND In general, DIAMOND is a sequence aligner for protein and translated DNA searches similar to NCBI BLAST, but much faster. In UGENE it is integrated for taxonomy classification of metagenomic NGS data. Reference databases UniRef50 and UniRef90 are provided by default. One can also build a custom database. 1.31.0 2018-08-17 65 0f53ebb8fb0d2f00f85d9b46fb280c49a9b6e005 ngs_classification.kraken Classification with Kraken Kraken is a tool for taxonomy classification of metagenomic NGS data. A MiniKraken reference database is provided by default with the tool. One can also build a custom database. 1.31.0 2018-08-17 80 f56fe5394f25c5ce30a80353563bc97c003e4d93 ngs_classification.wevote Classification with WEVOTE WEVOTE (WEighted VOting Taxonomic idEntification) is a tool for taxonomy classification of metagenomic NGS data, based on an ensemble of other classification methods (Kraken, CLARK, etc.). 1.31.0 2018-08-17 60 e4234512bced1d1ff7a1e30aacd7c19fc5b1f287 ngs_classification.metaphlan2 Classification with MetaPhlAn2 MetaPhlAn2 (METAgenomic PHyLogenetic ANalysis) is a tool for taxonomy classification of metagenomic NGS data. It relies on ~1M unique clade-specific marker genes. 1.32.0 2019-02-20 63 fd50b1a9a9f7c517289c764e08b76780d7497dd9 NGS.cistromeTool Cistrome External tools for the Cistrome workflow. 2.0.8.1 2020-03-18 2 full.tools.cistrome NGS.RScript tools.7z 6e2e19c32b4b2c2d002cf3f2123026641b130cad full.tools.blast+ BLAST+ BLAST+: Basic Local Alignment Search Tool. 2.10.1 2020-06-08 true 94 tools.7z de07ff3ebaedea66ccdd2a2b0c97c8458ed0e7d4 full.tools.bowtie Bowtie Bowtie is an ultrafast, memory-efficient short read aligner. 1.3.0 2020-07-22 true 92 tools.7z 601bfbbcee5a3eed47fbea15a6a28cb56c9668b2 full.tools.bowtie2 Bowtie2 Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. 2.4.2 2020-05-10 true 90 full.tools.python,full.tools.perl tools.7z 70ad9a32feac2adb8d161d5d5df57cc24bcd6333 full.tools.bwa BWA Burrows-Wheeler Aligner is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. 0.7.17 2017-11-07 true 88 tools.7z ed251b788890c808d86125401d77ddd85b5cae19 full.tools.fastqc FastQC FastQC - A high throughput sequence QC analysis tool. 0.11.9 2019-01-08 true 76 tools.7z bdf17dffb209c5ce00da0530e8aaafaf58cc8b63 full.tools.hmmer HMMER HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). 3.3.1 2020-07-25 true 75 tools.7z 3f440bd2fc004a4f09101c718b9eff74a2288e46 full.tools.mafft MAFFT MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <~200 sequences), FFT-NS-2 (fast; for alignment of <∼30,000 sequences), etc. 7.475 2020-11-26 true 73 tools.7z ef5bebcc9ae3dc1e00b586b166b22a58c423013f full.tools.trimmomatic Trimmomatic Trimmomatic is a flexible read trimming tool for Illumina NGS data. 0.39 2019-04-08 true 79 tools.7z 124f00f7c842d2ef1dee8a16f3752e1eb5acc585 full.tools.bedtools2 BEDtools Flexible tools for genome arithmetic and DNA sequence analysis. 2.29.2 2019-12-18 true 98 tools.7z 6040b54778dc48ff2d5a505e579924184326fcbb full.tools.bedGraphToBigWig bedGraphToBigWig Convert a bedGraph file to bigWig format. 4.0.0.0.1 2016-02-02 true 100 tools.7z 94d8354b74525fee43c729caeb75a50ebef1a682 full.tools.clustalo ClustalO Clustal Omega is the latest addition to the Clustal family. It offers a significant increase in scalability over previous versions, allowing hundreds of thousands of sequences to be aligned in only a few hours. It will also make use of multiple processors, where present. 1.2.4.0.1 2016-12-20 true 84 tools.7z 5a19f4cf98d5a575e7d88f82ccb55c908a5c7ace full.tools.clustalw ClustalW2 ClustalW2 is a general purpose DNA or protein multiple sequence alignment program for three or more sequences. 2.1.0.0.1 2010-11-17 true 82 tools.7z e9e61e530be49ddbb6114bedc38704f83568aeec full.tools.cufflinks Cufflinks Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. 2.0.2.0.1 2012-07-08 true 80 tools.7z 8cb5d6b191bba4e95af8808e02e8ca513e421030 full.tools.java Java "java" (JRE, Java Runtime Environment) is required to run several other external tools (e.g. FastQC and Trimmomatic). 1.8.0.192.1 2018-10-16 true 74 tools.7z f85002bedf2c64abf94343a2f8e16cc3349fdaf6 full.tools.mrbayes MrBayes MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. 3.2.3.0.1 2014-10-22 true 72 tools.7z 87de80000723a400fb31a32adac0dc10f68466bc full.tools.phyml PhyML A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. 20120412.0.0.0.1 2012-04-12 true 70 tools.7z e44d2ecb89ec65d04044a659520a3d898b8d90dd full.tools.samtools SAMtools SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. 0.1.19.0.1 2013-03-19 true 66 tools.7z dceed1ffdfbea736bc2bef8209806effbe1e6699 full.tools.snpEff SnpEff Genetic variant annotation and effect prediction toolbox. It annotates and predicts the effects of variants on genes (such as amino acid changes). 4.3.8.0.1 2016-12-16 true 64 tools.7z acdb6302cc6dde20ce3f7e062e8f134491dd8b8e full.tools.SPAdes SPAdes SPAdes is intended for both standard isolates and single-cell MDA bacteria assemblies. 3.14.1.0.1 2020-05-01 false 62 tools.7z eb6b025fb0d9c4af865ccf30660a3eadc2145b81 full.tools.stringtie StringTie StringTie is an assembler of RNA-Seq alignments into potential transcripts. 1.3.4.4.1 2018-02-25 true 80 tools.7z e10ef742f42cf6efb313d535fcd7d2dca2ac3370 full.tools.tcoffee T-COFFEE T-Coffee is a multiple sequence alignment package. 13.44.0 2020-09-15 true 58 tools.7z c102efb89c01b60c69bd5da884bfdb085a164fec full.tools.tophat 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. 2.1.1.0.1 2016-02-23 true 56 tools.7z f3ef09ca9cf34ab3dc331e993a0ed91191a84845 full.tools.vcftools VCFtools VCFtools is a program package designed for working with VCF files, such as those generated by the 1000 Genomes Project. The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files. 0.1.12.2.1 2014-08-04 true 54 tools.7z 0dd305c9ee5a408ae39c11e2565976c6913abe93 full.tools.CAP3 CAP3 CAP3 Sequence Assembly Program. 10-15-07-1 2010-07-15 true 86 tools.7z 60a265448fa6613a5a713ebbbcba3cc2ea0ced95 ngs_classification.clark.tools CLARK external tools Check this component to install CLARK executables. ngs_classification.taxonomy 1.2.4.2.1 2019-02-20 100 tools.7z 33b664f1fc988c4983359a8d4a28f268312ed99b ngs_classification.diamond.tools DIAMOND external tools Check this component to install DIAMOND executables. ngs_classification.taxonomy 0.9.22.0.1 2018-05-11 100 tools.7z 6d20fb4cc2db43dfeec9d5eabe46c746aaec728b ngs_classification.kraken.tools Kraken external tools Check this component to install Kraken executables. ngs_classification.taxonomy 1.0.0.0.1 2017-10-20 100 tools.7z 8bce66843e6214033f9d80f587480f8ecd4f805c ngs_classification.metaphlan2.tools MetaPhlAn2 external tools Check this item to install MetaPhlAn2 executables. full.tools.python, full.tools.bowtie2 2.7.7.0.1 2018-05-31 10 tools.7z 3af39761d545465f93742245646fd849f4a7eb87 NGS.RScript RScript external tool RScript is an alternative front end for use R scripts. 3.0.2.0.1 2013-09-25 3 tools.7z 26c2012b77d54dd6186d5930fa411fdd75b9c4bf full.tools.python Python Python is a widely used general-purpose, high-level programming language. 2.7.5.3 2013-05-15 true 68 python2.7z 971f77bfd17c7d3e50ada844195cf29934247f29 ugene.data Data folder Data folder with examples of various data. true 38.1 ugene 2021-03-26 100 true data.7z 17110a8acfbb2e04e6ace1fd3a7b1103a1336420 ugene.ugene UGENE executables UGENE executables. true true 38.1 2021-03-26 100 imageformats.7z,man1.7z,platforms.7z,plugins.7z,sqldrivers.7z,xcbglintegrations.7z,content.7z e2dc5284f8765fe077f69530f5bc2ef8e5d3f712