{AnyApplication}
1.0.0
true
full.tools.bedGraphToBigWig
bedGraphToBigWig
Convert a bedGraph file to bigWig format.
4
2016-02-02
true
100
tools.7z
557dbee115fa49f63f2a21ca643d6407ded197e5
full.tools.bedtools2
BEDtools
Flexible tools for genome arithmetic and DNA sequence analysis.
2.20.1
2016-02-02
true
98
tools.7z
d304e57cbb35f919a3a5f33ed108d38d919e18d9
full.tools.blast+
BLAST+
BLAST+: Basic Local Alignment Search Tool.
2.2.30
2016-02-02
true
94
tools.7z
857fbb22abd6a6092df6bf055aca32304984fb65
full.tools.bowtie
Bowtie
Bowtie is an ultrafast, memory-efficient short read aligner.
1.0.0
2016-02-02
true
92
tools.7z
3358dfe6573d0b8bb3412e5856f090448c488714
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
tools.7z
3b65d0a12ec00b0c3b10f638495806e33f8f0f3d
full.tools.CAP3
CAP3
CAP3 Sequence Assembly Program.
10-15-07
2010-07-15
true
86
tools.7z
2f79bd986d036ad6427aae2691048e7c3db88e06
full.tools.cistrome
Cistrome
External tools for the Cistrome workflow.
2.0.8
2016-02-02
true
56
tools.7z
36f1116f639ae15d7d473b22656d4b82484f173a
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.
1.2.1
2014-12-08
true
84
tools.7z
3a3cd6d4ce75f51ffbac0f6f1bca75179a6bcc7e
full.tools.clustalw
ClustalW2
ClustalW2 is a general purpose DNA or protein multiple sequence alignment program for three or more sequences.
2.1
2016-02-02
true
82
tools.7z
47875b5362c7c5be3daa28645eb4cddd539cf3dc
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
tools.7z
70d31e949ddc11b35b397b809c8ecebf71c20ffa
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
c3503211ef8e271c707b6748dbcafa714098c66c
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
tools.7z
be51ef6804b2ecd60d7193a99dddeb489c2ed919
full.tools.phyml
PhyML
A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood.
20120412
2012-04-12
true
70
tools.7z
f20edb31066428c519e3294f10490dd685af5b49
full.tools.python
Python
Python is a widely used general-purpose, high-level programming language.
2.7.5
2016-02-02
true
68
tools.7z
7c0a933c568e61878d3fb3131904af67303432e6
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
2016-02-02
true
66
tools.7z
67883c39be1f755982fe52c61c5c71ede9eb80ce
full.tools.SPAdes
SPAdes
SPAdes is intended for both standard isolates and single-cell MDA bacteria assemblies.
3.6.0
2015-08-17
false
62
tools.7z
0a868619d587796a108400400be3ce20a40f7fe4
full.tools.spidey
Spidey
Spidey is an mRNA-to-genomic alignment program.
1
2016-02-02
true
60
tools.7z
81988611ef7f247e7e4f0c24d0a11bf3f698c0e1
full.tools.tcoffee
T-COFFEE
T-Coffee is a multiple sequence alignment package.
11.00
2016-02-02
true
58
tools.7z
fe5d85faf7dd8da3a08fde1a755819973654b1ce
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.
2.0.8
2016-02-02
true
56
tools.7z
623a2e6539bad8a78516bc74efd92399f0c2c6ad
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
tools.7z
5ee8be27dabb784747499340ec4c4a58b375e197
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
e868412e02a1d5e781798d590aec2efe0d8a35ad
NGS.RScript
RScript external tool
RScript is an alternative front end for use R scripts.
3.0.2
2013-09-25
3
tools.7z
fa76481ab84ef60a1349f814c62ff5cbd8633c3b
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
tools.7z
99bd5a3f1e28d345526d52c5402b64deed6e4690
full
Full package additions
Full package additions.
1.29.0
2017-12-29
90
true
2c00243b89e27ef3a497b82787bf2f7a4c1af3bf
full.tools
External tools
External tools.
1.29.0
2017-12-29
90
true
3daf6575d26d06dcabb16c0df9f14a3dbaa5b401
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
6eef428b3efcfe3c500fd8073004930a321458f7
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).
4.3.7
2016-12-16
true
64
tools.7z
1a347e818f4b318e1a3319ffb80ffb588b1f6086
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
791a0f92b965acca972859320bb484c8329b875b
full.tools.trimmomatic
Trimmomatic
Trimmomatic is a flexible read trimming tool for Illumina NGS data.
0.38
2015-03-10
true
79
tools.7z
15c03430391cc91ca00f8db531b3e1d7b0f86854
full.tools.perl
Perl
Perl is a highly capable, feature-rich programming language.
5.24.3
2017-09-22
true
68
tools.7z
fbcc7842cc026653e2a8482cdda024d015135862
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
tools.7z
d0a0196504df33e5316cffa09503228007cfb89d
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
tools.7z
2cf8e13ee5cddef8e5397a4dda2cfc0d1958f86d
full.tools.fastqc
FastQC
FastQC - A high throughput sequence QC analysis tool.
0.11.8
2018-10-04
true
76
tools.7z
113c01d5310103f0b12f2c3c43a15d20263e5423
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
tools.7z
77853a100d49a1297f88af97ab96770346cfee4a
NGS.cistromeTool
Cistrome
External tools for the Cistrome workflow.
2.0.8.1
2020-03-18
2
full.tools.cistrome
NGS.RScript
tools.7z
29ab3e478915d6af6f50ef16c5baa1d3ed56fdef
ugene.data
Data folder
Data folder with examples of various data.
true
34.0
ugene
2020-03-18
100
true
data.7z
43c498afd5d02131f39afe30bb608b57d7e37f9c
ugene.ugene
UGENE executables
UGENE executables.
true
true
34.0
2020-03-18
100
imageformats.7z,platforms.7z,plugins.7z,sqldrivers.7z,content.7z
702d4457d66bc1f308b884d22cc7e15d6f8c079c
ugene
Standard package
Standard package contains executables and data of Unipro UGENE.
true
true
34.0.1
2020-05-15
100
73d75b81559d03f9fa7a829c3903f6b8a5715c9f