BioRuby protocols

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BioRuby specifications


Unique identifier OMICS_06833
Name BioRuby
Alternative name ruby-bio
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Stability Stable
Maintained Yes



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  • person_outline Toshiaki Katayama <>

Additional information

Tuto :

Publication for BioRuby

BioRuby in pipelines

PMCID: 4792137
PMID: 26976200
DOI: 10.1038/srep22745

[…] ng samples. the libraries were sequenced using an illumina hiseq 2000 instrument. redundancy was reduced according to umi, and the non-redundant reads were demultiplexed and trimmed by demlt tool in ruby-bio-gadget ( the demultiplexed reads were aligned to hg19 human reference genome, arraycontrol rna spikes and human ribosomal dna complete repeating unit […]

PMCID: 4466401
PMID: 26070213
DOI: 10.1371/journal.pone.0129154

[…] at a threshold more than fpkm = 1. the length and gc% distribution of all assembled unigenes are shown in fig and and in to calculate the gc content and basic statistics values used custom ruby/bioruby script [], the r/bioconductor package “shortread” [], and “biostrings” []., we performed a homology search against the ncbi nr protein database (, formatted […]

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BioRuby in publications

PMCID: 5945626
PMID: 29748565
DOI: 10.1038/s41467-018-03917-2

[…] (enst00000366794) using novoalign (novocraft technologies). mutations were called from the alignments using the ensembl variant effect predictor rest api (implementation: sequences were also translated and multiple alignments generated using clustal omega ( for the dense screen, coverage was calculated […]

PMCID: 5627052
PMID: 28878039
DOI: 10.1098/rsob.170129

[…] an e-value of 1 × 10−6. blast hits were then further analysed using an automated ruby script (available at each blast hit was translated using bioruby, and the open reading frame (orf) containing the blast high-scoring segment pair (hsp) was extracted. these orfs were then examined for the presence of a signal peptide using signal p 4.1 […]

PMCID: 5568602
PMID: 28830520
DOI: 10.1186/s12938-017-0356-5

[…] the corresponding transcriptome using bowtie2 [] with default parameters and the −a option to allow each read to map in all possible transcripts. mapped reads are then counted with bio-samtools from bioruby [] with the −f2 option to count only reads where both ends are mapping on the same transcript (only for illumina reads). the output is the tab-delimited, read count table where columns […]

PMCID: 5459929
PMID: 28449062
DOI: 10.1093/gigascience/gix029

[…] sequencing run was performed. we confirmed that there were no differences in the results of the modules that we used among the versions. we parsed the result files of fastqc (fastqc_data.txt) by the bioruby [] module bio-fastqc [], which we developed based on biogem []. the results from paired-end reads were concatenated by calculating the average values for each quality value, excluding values […]

PMCID: 5346198
PMID: 28293298
DOI: 10.1186/s13040-017-0130-z

[…] became a fertile new ground for programmers, who have gained access to an entirely new class of questions and challenges []. commonly used software packages are the bio*.org projects, such as bioruby [], bioperl [], biojava [] and biopython [], which have recently been assembled under the open bioinformatics foundation. each of these projects represents an international association […]

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BioRuby institution(s)
Department of Genome Informatics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Japan

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