BioKanga pipeline

BioKanga specifications

Information


Unique identifier OMICS_17237
Name BioKanga
Alternative name Bio K-mer Adaptive Next Generation Aligner
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C, C++
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Stuart Stephen <>

BioKanga IN pipelines

 (5)
2015
PMCID: 4558045
PMID: 26332397
DOI: 10.1371/journal.pone.0136899

[…] number srp061812., reads from all samples, including the mock-inoculated roots, were aligned to version 2 of the p. parasitica genome (phytophthora_parasitica_inra-310_2_supercontigs.fasta) using biokanga (http://code.google.com/p/biokanga/; v 1.12.1) with default parameters, which includes exhaustive search and allowance for five mismatches across the 50-bp reads. biokanga […]

2015
PMCID: 4558045
PMID: 26332397
DOI: 10.1371/journal.pone.0136899

[…] samples, including the mock-inoculated roots, were aligned to version 2 of the p. parasitica genome (phytophthora_parasitica_inra-310_2_supercontigs.fasta) using biokanga (http://code.google.com/p/biokanga/; v 1.12.1) with default parameters, which includes exhaustive search and allowance for five mismatches across the 50-bp reads. biokanga has been deliberately developed for non-model genome […]

2015
PMCID: 4558045
PMID: 26332397
DOI: 10.1371/journal.pone.0136899

[…] using biokanga (http://code.google.com/p/biokanga/; v 1.12.1) with default parameters, which includes exhaustive search and allowance for five mismatches across the 50-bp reads. biokanga has been deliberately developed for non-model genome analysis and incorporates extensive optimisation to deal with increased uncertainty when aligning to non-reference genomes. reads […]

2015
PMCID: 4618961
PMID: 26493707
DOI: 10.1186/s12864-015-2105-0

[…] by solexaqa scripts (http://solexaqa.sourceforge.net/) to a minimum quality value of 30 and a minimum length of 70. alignments of rna reads from resistant and sensitive nils were performed using the biokanga suite (a tool developed at csiro, not published) with 2 mismatches allowed per read. paired reads for all reads aligned to the defined region containing the fcr locus were retrieved […]

2014
PMCID: 4236173
PMID: 25405461
DOI: 10.1371/journal.pone.0113309

[…] was performed with a maximum of 2 mismatches per read. minimum coverage for the declaration of an snp was 4 nucleotides. snps between the resistant and susceptible isolines were identified using the biokanga snpmarkers sub-process with a minimum 90% score, i.e., the percentage of a given nucleotide at a snp position is at least 90% in the resistant or susceptible isolines., degs and expressed […]

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