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Number of citations per year for the bioinformatics software tool bíogo

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This map represents all the scientific publications referring to bíogo per scientific context
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bíogo specifications


Unique identifier OMICS_16273
Name bíogo
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License BSD 3-clause “New” or “Revised” License
Computer skills Advanced
Version 1.0.1
Stability Stable
Maintained Yes




No version available



  • person_outline Daniel Kortschak
  • person_outline David Adelson

Publication for bíogo

bíogo citations


Superior ab initio identification, annotation and characterisation of TEs and segmental duplications from genome assemblies

PLoS One
PMCID: 5851578
PMID: 29538441
DOI: 10.1371/journal.pone.0193588

[…] ted in the genome, i.e. that are rarely or never found in tandem, and are usually mobile elements such as retrotransposons []. Genome sequences were pairwise aligned using krishna (https://github.com/biogo/examples/krishna) with default parameters set at 94% sequence identity (-dpid) and a minimum alignment length (-dplen) of 250bp for most cases, except bearded dragon and chicken, which used -dpi […]


Delivery of biotinylated IGF 1 with biotinylated self assembling peptides combined with bone marrow stem cell transplantation promotes cell therapy for myocardial infarction

PMCID: 5639271
PMID: 29042931
DOI: 10.3892/etm.2017.4982

[…] as from Abcam (Cambridge, MA, USA). Monoclonal antibody anti-cardiac troponin T (cTnT; catalogue no. LI4C00702) was purchased from Shanghai Linc-Bio Science Co. Ltd. (Shanghai, China; http://lzhenyul.biogo.net/sell/typeid-39.shtml), Polyclonal antibody anti-connexin-43 (CX-43; catalogue no. RLT1044) was purchased from Ruiying Biological (Suzhou, Jiangsu, China; http://www.rlgene.com/). Polyclonal […]


Energy Efficient Routes for the Production of Gasoline from Biogas and Pyrolysis Oil—Process Design and Life Cycle Assessment

PMCID: 5384482
PMID: 28405056
DOI: 10.1021/acs.iecr.6b04611

[…] As stated above, the BIOGO project explores a different route to produce gasoline. Instead of following the conventional methanol-to-gasoline (MtG) route, it looks at gasoline production from biogas and pyrolysis oil.The […]


SeqKit: A Cross Platform and Ultrafast Toolkit for FASTA/Q File Manipulation

PLoS One
PMCID: 5051824
PMID: 27706213
DOI: 10.1371/journal.pone.0163962

[…] least amount of time. The FASTA/Q parsing module of seqtk, klib [], is highly optimized, which makes it very efficient in terms of execution time and memory usage. Interestingly, while SeqKit and the biogo package[] were both written in Go, SeqKit was approximately 9~11 times faster than the biogo package for FASTA parsing, which indicates the efficiency of the SeqKit algorithm.SeqKit required far […]


HENMT1 and piRNA Stability Are Required for Adult Male Germ Cell Transposon Repression and to Define the Spermatogenic Program in the Mouse

PLoS Genet
PMCID: 4619860
PMID: 26496356
DOI: 10.1371/journal.pgen.1005620

[…] e loss of HENMT1 function leads to instability of both MILI and MIWI associated piRNAs.To further explore the precise nature of RNA shortening we examined a variety of piRNA characteristics using the bíogo bioinformatics toolkit. Initially, wild type piRNAs were analysed according to alignment length and genomic location. This involved filtering aligned reads by sequence, mapping quality, and piRN […]


Genetic Diversity and Structure of Sinopodophyllum hexandrum (Royle) Ying in the Qinling Mountains, China

PLoS One
PMCID: 4198291
PMID: 25333788
DOI: 10.1371/journal.pone.0110500

[…] Total genomic DNA was extracted from frozen leaves by using a plant genomic DNA rapid extraction kit (Spin-column) (BioTek Corporation, Beijing, China; http://bioteke.biogo.net/). The extracted DNA was quantified by comparing with known DNA of standard quantity (Lambda DNA) through electrophoresis in ethidium bromide-stained 1.0% agarose gels (Gene Genius Bio Imagi […]

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bíogo institution(s)
School of Molecular and Biomedical Science, University of Adelaide, Adelaide, WA, Australia
bíogo funding source(s)
Supported by The University of Adelaide and The National Health and Medical Research Council [grant number 1011334].

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