{AnyApplication} 1.0.0 true full.tools.bedGraphToBigWig bedGraphToBigWig Convert a bedGraph file to bigWig format. 4 2016-02-02 true 100 Contents.7z 52650db425bdccdeab3cc8b6b2952f878b438dd8 full.tools.bedtools2 BEDtools Flexible tools for genome arithmetic and DNA sequence analysis. 2.20.1 2016-02-02 true 98 Contents.7z bd154ddd184e179ac719c27b4663d37eadfc2fec full.tools.blast+ BLAST+ BLAST+: Basic Local Alignment Search Tool. 2.2.30 2016-02-02 true 94 Contents.7z fc93e3b788f0e4b0d0fce930637d7e9cba361e67 full.tools.bowtie Bowtie Bowtie is an ultrafast, memory-efficient short read aligner. 1.0.0 2016-02-02 true 92 Contents.7z 60276613ed2c1e285f091d982434f8fd070ad2ae 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. 0.7.12 2016-02-02 true 88 Contents.7z 7d36468c1c88c6f97c801c77209ac5374b10a63a full.tools.CAP3 CAP3 CAP3 Sequence Assembly Program. 10-15-07 2010-07-15 true 86 Contents.7z 967904b8393bdd3eae0b67a8464f35083ede31c1 full.tools.cistrome Cistrome External tools for the Cistrome workflow. 2.0.8 2016-02-02 true 56 Contents.7z 8e7c8194a27c1685a2c788f55f65c53d93ae6ee1 full.tools.cufflinks Cufflinks Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. 2.0.2 2016-02-02 true 80 Contents.7z 770bc1965d51fdcefeebd4a8e96c727f7e805899 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 Contents.7z 3d9d0f1ee8ab0778d196b7558b50b5a5c5210d00 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). 3.1 2015-05-05 true 75 Contents.7z 195930a899e8ed17b349d730b2ee6da1ebf909e2 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 2016-02-02 true 72 Contents.7z 0fae0937f3727a6ffbfd9f53d124a36ba83f2332 full.tools.perl Perl Perl is a highly capable, feature-rich programming language. 5.10.0.5 2013-06-24 true 68 b561347243c1db592f96a584d32147b8646bd498 full.tools.phyml PhyML A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. 20120412 2012-04-12 true 70 Contents.7z 11f669dd70a0227e52a9cdd25bf2f17a16001c5d 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. 0.1.19-1 2016-02-02 true 66 Contents.7z 451e264c8780000891cd0927950282afaeec0053 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 2016-12-15 true 64 Contents.7z 1be723f030bf0e6902c2e43eff978b7f0df0dfc5 full.tools.spidey Spidey Spidey is an mRNA-to-genomic alignment program. 1 2016-02-02 true 60 c540cb8056b04aed47a10441e8b9f0038e8d1625 full.tools.tcoffee T-COFFEE T-Coffee is a multiple sequence alignment package. 11.00 2016-02-02 true 58 Contents.7z eb27c9269becdf791960012bec8d7cee599c38bc 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 2016-02-02 true 54 Contents.7z 13acfaf56ed8c62cb450f6bdf085e572779caf77 NGS.cistrome Data for the Cistrome workflow (for ChIP-Seq) Sample data for the Cistrome workflow. 1.0.0 2010-07-15 1 Contents.7z 2ac8ad766526504304bfc2ec0947a28680d4de00 NGS.RScript RScript external tool RScript is an alternative front end for use R scripts. 3.0.2 2013-09-25 3 Contents.7z 418ad3ad3573bccf3619df41b2c1246967a1ee24 full Full package additions Full package additions. 1.29.0 2017-12-29 90 true 1100cda14798c3d656c52058f9535cdfddab965d full.tools External tools External tools. 1.29.0 2017-12-29 90 true 2cc816af31a3ac0ff90280717292f7363cd53fd8 ugene Standard package Standard package contains executables and data of Unipro UGENE. true true 1.29.0 2017-12-29 100 3a23d63c1995336a96c2206ab5920646313f32fd 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 6ce290b39b0fb64122e5ef9eb028bc56d3b26a9b full.tools.stringtie StringTie StringTie is an assembler of RNA-Seq alignments into potential transcripts. 1.3.4.4 2018-02-25 true 80 Contents.7z 8b90b85069a93bbb92af30ad14b818531cab9b97 full.tools.trimmomatic Trimmomatic Trimmomatic is a flexible read trimming tool for Illumina NGS data. 0.38 2015-03-10 true 79 Contents.7z 7723a9a26950e303be80560c5f5a0d5023416268 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 77c5be407745640b16ce1dd51d4597879dc440f8 ngs_classification.wevote.tools WEVOTE external tools Check this component to install WEVOTE executables. ngs_classification.taxonomy 1.0.0 2018-01-29 100 Contents.7z 40ccd06f187660212f564673a0e3db8b3a222cf6 ngs_classification.diamond.tools DIAMOND external tools Check this component to install DIAMOND executables. ngs_classification.taxonomy 0.9.22 2018-05-11 100 Contents.7z 1cab091dc4435cc88fe46fc8a8eb91e1ee91bf64 ngs_classification.kraken.tools Kraken external tools Check this component to install Kraken executables. ngs_classification.taxonomy 1.0.0 2017-10-20 100 Contents.7z 11724f4caa7faab7d31bb75cdde5598f8a879177 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 8ad26ea909992acac4a2437630a183b1a96b085c 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 94bd5b9c0663d8ab4f2932ecd375f360d1008568 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 d27b50fd3eda84924fab98fdd826b84adb341a43 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 574f00a4fa59a4cea8dbd641cc4805304e546443 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 a6d2fde7934a62d8d83aee2da19758adc89699b2 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 d7138bc991e61afb072b4e4821929620baebec36 full.tools.python Python Python is a widely used general-purpose, high-level programming language. 2.7.5.1 2016-02-02 true 68 Contents.7z 32bc45f91197a1add4bc6db0fae310a8409b6958 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 2018-07-10 true 74 Contents.7z 66d9a6fe71a79ffd0baa3c93f8a23fea8cd21158 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 f965d015cd960ed7c0d28bc451fdd49e3394f148 ngs_classification.metaphlan2.tools MetaPhlAn2 external tools Check this item to install MetaPhlAn2 executables. full.tools.python, full.tools.bowtie2 2.7.7 2018-05-31 10 Contents.7z 59161a654d3a4a7c37139f7753e3df20794d9dab ngs_classification.clark.tools CLARK external tools Check this component to install CLARK executables. ngs_classification.taxonomy 1.2.4.2 2018-02-27 100 Contents.7z ccffaac4e03ced5aec8e204b1623bb72ad4c37b0 full.tools.bowtie2 Bowtie2 Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. 2.3.4.3 2018-09-17 true 90 full.tools.python,full.tools.perl Contents.7z 863e890a37b24f33cef01cc5a44e6ea77865df90 full.tools.fastqc FastQC FastQC - A high throughput sequence QC analysis tool. 0.11.8 2018-10-04 true 76 Contents.7z 4fc8fd5b1059c678ee97734dcda398b80e52ef68 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 2016-02-23 true 56 Contents.7z 4035d74bc7b6ccb0534c24336acc2a5613719bf2 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. 7.450 2019-09-23 true 73 Contents.7z c5e62fd0e8ebc1e4001da143ffdf838ba9be37ec NGS.cistromeTool Cistrome External tools for the Cistrome workflow. 2.0.8 2020-03-18 2 full.tools.cistrome NGS.RScript Contents.7z 379578a44db1f66850bd6ce69de3ae21e25a3298 full.tools.clustalw ClustalW2 ClustalW2 is a general purpose DNA or protein multiple sequence alignment program for three or more sequences. 2.1.1 2016-02-03 true 82 Contents.7z 64924dc3e1fd9e036000412b954f4a909aa032ac 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. 1.2.3 2016-07-20 true 84 Contents.7z 5d69052ab2f4030c8fd2bb3e78137c1ff4ad2930 full.tools.SPAdes SPAdes SPAdes is intended for both standard isolates and single-cell MDA bacteria assemblies. 3.14.1 2020-05-01 false 62 Contents.7z 55e8e1bc68532d6b3808f2d007a245c44d8ed6bb ugene.data Data folder Data folder with examples of various data. true 36.0 ugene 2020-09-21 100 true Contents.7z c2bfdbf161e6d4c07fcb9aa46b5e745470ae2f55 ugene.ugene UGENE executables UGENE executables. true true 36.0 2020-09-21 100 Contents.7z c4b7554405aea958a9abfdb7d3be53e432222138