Bio-Linux protocols

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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

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Publication for Bio-Linux

Bio-Linux in pipelines

 (2)
2015
PMCID: 4318436
PMID: 25636363
DOI: 10.1186/s12864-015-1254-5

[…] preparation kit, multiplexed with 24 samples per lane and sequenced using an illumina hiseq 2500, to generate 100 bp paired reads., all analyses were carried out on a local server running the nebc bio-linux 7 environment []. remaining illumina adaptor sequences were removed and the first 12 bp of all raw sequence reads were trimmed to remove 5' bias caused by non-random hexamer priming [] […]

2015
PMCID: 4540916
PMID: 26135867
DOI: 10.1128/JCM.01357-15

[…] supplemental material), with the ksnp v2 software suite (, ) with standard settings and a k-mer value of 31, and the parsnp program from the harvest suite () with the “-a 13 -c -x” switches, within bio-linux ()., alignments were made with clustalx2 and mega v5.2 (, ). assignment of multilocus sequence types was done by downloading 1,409 concatenated seven-gene alleles (atpa, efp, muty, ppa, […]


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Bio-Linux in publications

 (24)
PMCID: 5729454
PMID: 29255485
DOI: 10.1186/s13068-017-0989-4

[…] 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 […]

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

[…] 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 […]

PMCID: 5602524
PMID: 29246301
DOI: 10.1016/j.omtn.2017.08.010

[…] ligated at the novel 5′ ends generated on the hcv genome by slicer action resulting into an ∼80-bp read length., 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, […]

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

[…] with a template‐positive isps and run on the ion proton sequencer., 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). the unmapped reads, generated […]

PMCID: 5431808
PMID: 28496194
DOI: 10.1038/s41598-017-01808-y

[…] command with the parameters –w 50 –s 20 –m 2. chimera filtering were performed by “usearch -uchime_denovo” in usearch program which base on uchime algorithm. the above steps were completed using the bio-linux 8 system, which integrates all of the above-mentioned tools. short reads (<250 bp) were filtered using the “biostrings” package in r software (3.1.2) with the bioconductor environment. […]


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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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