Galaxy statistics

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Citations per year

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Popular tool citations

chevron_left Read quality control SNP detection SNV detection Alignment evaluation Known transcript quantification File format conversion Workflow management systems Differential expression Sequence alignment visualization Network visualization De novo transcriptome assembly Duplicate read removal Structural motif detection File filtering Indel detection Peak calling Tag count Variant detection Variant detection Depth of coverage File intersection File sorting chevron_right
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Protocols

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Galaxy specifications

Information


Unique identifier OMICS_01141
Name Galaxy
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Subtool


  • FASTQ Groomer

Maintainer


  • person_outline Daniel Blankenberg <>

Publications for Galaxy

Galaxy in pipelines

 (111)
2018
PMCID: 5788975
PMID: 29379011
DOI: 10.1038/s41467-017-02706-7

[…] by smrt analysis software (v2.3.0) pipelines to produce reads-of-inserts (rois) representing multiplexed pcr amplicon sequences in fastq format. all downstream workflows were performed using the galaxy web-based platform for genome data analysis–, unless specified. reads were filtered by length and demultiplexed. sequences were then aligned with bwa-mem to a custom reference representing […]

2018
PMCID: 5788982
PMID: 29379047
DOI: 10.1038/s41598-018-19820-1

[…] resulting reads were trimmed at both ends. nucleotide positions with a score lower than 20 were also masked (replaced by an n). these analyses were performed using the fastq tools implemented in the galaxy platform,. the total number of reads for each transcriptome is presented in supplementary table . to assess the changing rate of new gene detection as a function of sequencing sampling […]

2018
PMCID: 5838928
PMID: 29527141
DOI: 10.1186/s12014-018-9188-y

[…] intensity distribution and calculating the pearson correlation coefficient. functional classification of the identified proteins was performed with panther (v11.1) [, ]. the open, web-based platform galaxy [, ] was used to calculate the identified proteins’ molecular weight, isoelectric point and gravy score with biopython [] as well as potential transmembrane domains with a hidden markov model […]

2018
PMCID: 5853447
PMID: 29568283
DOI: 10.3389/fmicb.2018.00356

[…] the institute for molecular medicine finland (fimm). rna-seq data analysis was mainly performed on a 64-cores local unix server and computation-intensive read alignment steps were performed on the galaxy instance of freiburg university (cock et al., ; afgan et al., ). in short, the quality of the raw reads was checked using fastqc v0.11.4 (andrews, ), and reads were demultiplexed […]

2018
PMCID: 5882135
PMID: 29614079
DOI: 10.1371/journal.pgen.1007287

[…] hi seq2500 at the beijing genomic institute (sacramento, ca, usa) and wideseq at purdue genomics core facility (https://www.purdue.edu/hla/sites/genomics/wideseq-2/), and were assembled using galaxy [,]. we identified and annotated the repetitive elements in the sr21 region using the triticeae repeat sequence database (http://wheat.pw.usda.gov/itmi/repeats/blastrepeats3.html) […]


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Galaxy in publications

 (585)
PMCID: 5954162
PMID: 29765130
DOI: 10.1038/s41598-018-25827-5

[…] variant locus. variants were annotated and analysed using ingenuity variant analysis (iva) software (qiagen, redwood city, ca, usa), mutationtaster2, snpeff, seattleseq annotation server, and galaxy (via usegalaxy.org). allele frequencies and additional annotations were drawn from 1000 genomes project, nhlbi go exome sequencing project (esp), seattle, wa […]

PMCID: 5945652
PMID: 29749381
DOI: 10.1038/s41598-018-25921-8

[…] for bmi1-overexpressing and control enscs, and from 13–59 million mapped reads for bmi1-overexpressing and control anscs. gene expression was analyzed and compared using tophat and cufflinks in the galaxy server package., gene expression was strongly correlated between enscs and anscs (fig. ). we also compared expression changes caused by bmi1 overexpression in anscs at one week and four weeks […]

PMCID: 5942802
PMID: 29742123
DOI: 10.1371/journal.pone.0196178

[…] we tracked their v4 hypervariable sequences in the total pool of v4 sequences in each corresponding holobiont microbiomes. we used different similarity identity thresholds using usearch tool from galaxy platform []. this tool is based on usearch and uclust algorithms []. these thresholds varied from 100% to 98.00%, i.e. from 0 to 5 different nucleotides in the sequences aligned (252 bp […]

PMCID: 5946028
PMID: 29780403
DOI: 10.3389/fgene.2018.00154

[…] above from both the 5′ and 3′ ends of the pri-mirnas, and then search for overlaps with pol2 chip-seq data. notably, the median length of human pri-mirnas is approximately 41 kb, mouse 36 kb (). the galaxy website was used to find overlaps and join different datasets into single files for correlation studies (). for chip-seq, we considered pol2 peaks on both dna strands. for rna-seq, […]

PMCID: 5919700
PMID: 29698473
DOI: 10.1371/journal.pone.0196590

[…] for gene models fully compatible with the format accepted by the first script, a reads mapping session was performed using tophat followed by the cufflinks and cuffmerge tools (table b in ), on the galaxy open source web-based platform []. cuffmerge output gtf file and tophat output bam alignment files were exported and used as input for the first and the second python scripts, respectively. […]


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Galaxy institution(s)
Department of Biology, Johns Hopkins University, Baltimore, MD, USA; Department of Computer Science, Albert-Ludwigs-University, Freiburg, Freiburg, Germany; Institut Curie, PSL Research University, Paris, France; Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA, USA; Center for Biological Systems Analysis (ZBSA), University of Freiburg, Freiburg, Germany; Department of Pathology, Erasmus Medical Center, Rotterdam, The Netherlands; Department of Biomedical Engineering, Oregon Health and Science University, OR, USA; Earlham Institute, Norwich Research Park, Norwich, UK; Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
Galaxy funding source(s)
Supported by the National Human Genome Research Institute, National Institutes of Health [HG006620, HG005133, HG004909 and HG005542]; NSF [DBI 0543285, 0850103 and 1661497]; Huck Institutes for the Life Sciences at Penn State; and, in part, under a grant with the Pennsylvania Department of Health using Tobacco Settlement Funds.

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