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Rockhopper specifications


Unique identifier OMICS_08790
Name Rockhopper
Software type Pipeline/Workflow
Interface Graphical user interface
Restrictions to use None
Input data FASTQ, QSEQ, FASTA, SAM, or BAM files
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License GNU General Public License version 2.0
Computer skills Medium
Version 2.0
Stability Stable
Maintained Yes


No version available


  • person_outline Brian Tjaden

Publications for Rockhopper

Rockhopper citations


Determining the Specificity of Cascade Binding, Interference, and Primed Adaptation In Vivo in the Escherichia coli Type I E CRISPR Cas System

PMCID: 5904413
PMID: 29666291
DOI: 10.1128/mBio.02100-17

[…] tSeq 2.0 kit (Epicentre). Sequencing was performed using an Illumina Next-Seq instrument (Wadsworth Center Applied Genomic Technologies Core). Differential RNA expression analysis was performed using Rockhopper (version 2.03) with default parameters (). Differences in RNA levels were considered statistically significant for genes with false-discovery-rate (q) values of ≤0.01. […]


First quantification of subtidal community structure at Tristan da Cunha Islands in the remote South Atlantic: from kelp forests to the deep sea

PLoS One
PMCID: 5875861
PMID: 29596484
DOI: 10.1371/journal.pone.0195167

[…] or the presence of additional species. This extension yielded 106 additional individuals, new species included a single bluefish (Hyperoglyphe antarctica) of 84.8 cm at Nightingale Island, a northern rockhopper penguin (Eudyptes moseleyi) of 36.7 cm, and 5 dusky dolphins (Lagenorhynchus obscurus) at Gough Island. There is a large population of northern rockhopper penguins on Gough Island and large […]


Inter replicon Gene Flow Contributes to Transcriptional Integration in the Sinorhizobium meliloti Multipartite Genome

PMCID: 5940162
PMID: 29563186
DOI: 10.1534/g3.117.300405
call_split See protocol

[…] e generated with the heatmap.2 function in the gplots package of R (), and the clustering performed using average linkage with a Pearson correlation distance. Operon prediction was performed with the Rockhopper software () using the raw RNA-seq data generated in this study (File S5). Genes were classified as core, accessory, or dispensable based on a previously published pangenome analysis (). The […]


Piggy: a rapid, large scale pan genome analysis tool for intergenic regions in bacteria

PMCID: 5890482
PMID: 29635296
DOI: 10.1093/gigascience/giy015
call_split See protocol

[…] size 31 and –bootstrap-samples 100), and Sleuth [] was used to normalize and filter the counts produced by Kallisto. These counts were then log10 transformed, and major axis regression was performed. Rockhopper2 [] was used to produce an operon map for each strain by grouping adjacent genes with similar expression profiles together into operons. […]


Identification of a novel gene in ROD9 island of Salmonella Enteritidis involved in the alteration of virulence associated genes expression

PMCID: 5955183
PMID: 29130383
DOI: 10.1080/21505594.2017.1392428
call_split See protocol

[…] control was performed using the NGS QC Toolkit to ensure that at least 70% of the total bases per read had a Phred quality score of 20 or higher. Bacterial transcriptome analysis was performed using Rockhopper62 with reads mapped to the genome of S. Enteritidis P125109 (Acc No. AM933172.1) with the average number of HQ reads profiled to WT and ΔSEN1005 being 32.58 and 31.04 million respectively a […]


Comparison of Salmonella enterica Serovars Typhi and Typhimurium Reveals Typhoidal Serovar Specific Responses to Bile

Infect Immun
PMCID: 5820949
PMID: 29229736
DOI: 10.1128/IAI.00490-17
call_split See protocol

[…] nusual G-C bias using FastQC. The median Phred score for all samples was >34. To permit comparison between strains, sequenced reads for each strain were mapped to the Ty2 genome (NC_004631) using the Rockhopper tool () with default parameters (see Data Sets S1 to S3 in the supplemental material). The read alignment coverage for each sample can be found in Table S2 in the supplemental material. The […]


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Rockhopper institution(s)
Computer Science Department, Wellesley College, Wellesley, MA, USA

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