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iGenomes specifications


Unique identifier OMICS_20217
Name iGenomes
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes


  • Bacteria
    • Mycobacterium tuberculosis
  • Invertebrates
    • Caenorhabditis elegans
    • Drosophila melanogaster
  • Mammals
    • Bos taurus
  • Plants and Fungi
    • Glycine max
    • Oryza sativa
    • Saccharomyces cerevisiae
    • Schizosaccharomyces pombe
    • Zea mays
  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus
    • Rattus norvegicus
  • Vertebrates
    • Danio rerio
    • Gallus gallus

iGenomes citations


Distinct epigenetic landscapes underlie the pathobiology of pancreatic cancer subtypes

Nat Commun
PMCID: 5958058
PMID: 29773832
DOI: 10.1038/s41467-018-04383-6

[…] build and gene counts with the HTSeq software 0.5.3p9 (http://www.huber.embl.de/users/anders/HTSeq/doc/overview.html) using gene annotation files obtained from Illumina (http://cufflinks.cbcb.umd.edu/igenomes.html). RNA-seq reads were also mapped using STAR with the proposed ENCODE parameters and XENOME on the human hg19 and mouse mm10 genomes and transcript annotation (Ensembl 75). Gene counts we […]


IFN λ and microRNAs are important modulators of the pulmonary innate immune response against influenza A (H1N2) infection in pigs

PLoS One
PMCID: 5909910
PMID: 29677213
DOI: 10.1371/journal.pone.0194765
call_split See protocol

[…] plied for the remaining sequencing data processing [], using the mapper module to collapse trimmed reads and Bowtie v. 1.0.0 [] for the mapping of reads to a pre-built indexed porcine genome from the iGenomes collection from Illumina (‘susScr3’ from UCSC built on the Sscrofa10.2 genome assembly [], downloaded January 27th 2015 from here: https://support.illumina.com/sequencing/sequencing_software/ […]


Orientation dependent Dxz4 contacts shape the 3D structure of the inactive X chromosome

Nat Commun
PMCID: 5899087
PMID: 29654302
DOI: 10.1038/s41467-018-03694-y
call_split See protocol

[…] raries were sequenced as single-end reads of 75 bp in length (Supplementary Table ). RNA-seq reads were mapped to the UCSC mm10 (NCBI build v38) refSeq transcriptome as downloaded and packaged in the iGenomes reference sequences and annotation files on July 17, 2015. (https://support.illumina.com/sequencing/sequencing_software/igenome.html). Tophat2 (v 2.0.12) (calling bowtie2 (v2.2.3)) was used t […]


Somatic genome editing with the RCAS TVA CRISPR Cas9 system for precision tumor modeling

Nat Commun
PMCID: 5899147
PMID: 29654229
DOI: 10.1038/s41467-018-03731-w

[…] d 20 multihits; transcripts quantification and differential expression were calculated with Cufflinks 2.2.1, using the mouse NCBI37/mm9 transcript annotations from https://ccb.jhu.edu/software/tophat/igenomes.shtml. GSEAPreranked was used to perform gene set enrichment analysis of the described gene signatures on a pre-ranked gene list, setting 1000 gene set permutations. Fusion transcripts were i […]


Transient reduction of DNA methylation at the onset of meiosis in male mice

PMCID: 5883305
PMID: 29618374
DOI: 10.1186/s13072-018-0186-0
call_split See protocol

[…] During the alignment, we provided a transcriptome file that contained gene annotation. The reads were processed based on NCBI37/mm9 mouse genome and UCSC RefSeq gene annotation obtained from Illumina iGenomes (July 2015).We used HTSeq package to count sequencing reads that overlap with gene transcriptome []. Specifically, we used command. The output […]


Evaluation of the ISL1 gene in the pathogenesis of bladder exstrophy in a Swedish cohort

Hum Genome Var
PMCID: 5874392
PMID: 29619236
DOI: 10.1038/hgv.2018.9

[…] mming of reads. Between 73 and 85% of reads from individual samples mapped to known exons (median 83.15%). The Ensembl annotation and genome sequence version GRCh37 used are available on the Illumina iGenomes web page (http://support.illumina.com/sequencing/sequencing_software/igenome.html). Star v. 2.5.1.b with the default settings was used to map the short reads to the reference genome. Read pai […]


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