Bio-Linux statistics

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Citations per year

Number of citations per year for the bioinformatics software tool Bio-Linux
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Tool usage distribution map

This map represents all the scientific publications referring to Bio-Linux per scientific context
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Protocols

Bio-Linux specifications

Information


Unique identifier OMICS_01137
Name Bio-Linux
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Version 8.0
Stability Stable
Maintained Yes

Versioning


No version available

Publication for Bio-Linux

Bio-Linux citations

 (40)
library_books

Genetic diversity of equine herpesvirus 1 isolated from neurological, abortigenic and respiratory disease outbreaks

2018
PMCID: 5947664
PMID: 29423949
DOI: 10.1111/tbed.12809

[…] Read data were assessed for quality using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) running within Bio‐Linux 7 (Field et al., ). Adapter sequences were removed from the reads, which were then quality filtered and trimmed using Trim Galore v. 0.3.3 (http://www.bioinformatics.babraham.ac.uk/projects/ […]

library_books

The effect of temperature and retention time on methane production and microbial community composition in staged anaerobic digesters fed with food waste

2017
Biotechnol Biofuels
PMCID: 5729454
PMID: 29255485
DOI: 10.1186/s13068-017-0989-4

[…] × 300 paired-end sequencing (Illumina, San Diego, CA, USA).Sequence processing and data analysis were performed on an ASUS laptop with 2.6 GHz quad-core Intel Core i7-6700HQ CPU and 16 GB RAM running Bio-Linux 8 []. First, the paired-end reads were merged using PEAR version 0.9.6 [] specifying a maximum assembly length of 575, a minimum assembly length of 400, and a minimum overlap of 50 nucleotid […]

library_books

Effects of Lactobacillus acidophilus on gut microbiota composition in broilers challenged with Clostridium perfringens

2017
PLoS One
PMCID: 5708699
PMID: 29190649
DOI: 10.1371/journal.pone.0188634

[…] eans of the Uparse software and removed. Then the Effective Tags were obtained and applied to further analyses.Uparse was used to select operational taxonomic units (OTUs) at 97% similarity [] on the Bio-Linux platform. Representative sequences were processed via the QIIME pipeline []. LCA alignment assignment was carried out based on the Silva database []. Resampling according to the minimal sequ […]

library_books

Indigenous species barcode database improves the identification of zooplankton

2017
PLoS One
PMCID: 5627919
PMID: 28977035
DOI: 10.1371/journal.pone.0185697

[…] tform [] to filter low-quality reads and to discard reads with more than two mismatches in primer sequence. Chimeras were identified and removed by UCHIME []. The above steps were completed using the Bio-Linux 8 system, which integrates all of the above-mentioned tools []. Short reads (< 200 bp) were filtered using the “Biostrings” package in R with the Bioconductor environment []. The high qualit […]

library_books

Profiling the Mismatch Tolerance of Argonaute 2 through Deep Sequencing of Sliced Polymorphic Viral RNAs

2017
Mol Ther Nucleic Acids
PMCID: 5602524
PMID: 29246301
DOI: 10.1016/j.omtn.2017.08.010

[…] All the bioinformatics analyses for this project were undertaken on a Bio-Linux 8 workstation within an Ubuntu Linux 14.04 LTS base and bioinformatics packages updated to their latest available versions using the default update advisor. Additional packages, such as Cuta […]

library_books

CXCL12α/SDF‐1 from perisynaptic Schwann cells promotes regeneration of injured motor axon terminals

2017
PMCID: 5538331
PMID: 28559442
DOI: 10.15252/emmm.201607257

[…] Bioinformatics analysis was carried out using several command line software included in Bio‐Linux (http://nebc.nerc.ac.uk/tools/bio-linux/bio-linux-7-info). Using Star aligner, the reads, previously filtered for quality and length, were processed and aligned to mouse genome (mm10 version […]


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Bio-Linux institution(s)
The NERC Environmental Bioinformatics Centre, Oxford Centre for Ecology and Hydrology, Oxford, UK; the Molecular Evolution and Bioinformatics Section, Oxford Centre for Ecology and Hydrology, Oxford, UK; the Bioinformatics Support Unit, Institute for Cell and Molecular Biosciences, University of Newcastle upon Tyne, Newcastle, UK; CEH Computing Services, Oxford Centre for Ecology and Hydrology, Oxford, UK

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