{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
ugene.data
Data folder
Data folder with examples of various data.
true
37.1
ugene
2020-01-04
100
true
data.7z
b2716912f4659adbdcf06bb3a8fecf34dc935b91
ugene.ugene
UGENE executables
UGENE executables.
true
true
37.1
2020-01-04
100
imageformats.7z,man1.7z,platforms.7z,plugins.7z,sqldrivers.7z,content.7z
f687cd821b22dffec68078384faa222a72338561
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