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marginAlign specifications

Information


Unique identifier OMICS_07582
Name marginAlign
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input format BAM
Biological technology Oxford Nanopore
Operating system Unix/Linux
Programming languages Python
License MIT License
Computer skills Advanced
Stability Stable
Requirements
git, pip/virtualenv
Maintained Yes

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Documentation


Publication for marginAlign

marginAlign in publications

 (3)
PMCID: 5889714
PMID: 29431738
DOI: 10.1038/nbt.4060

[…] coverage of the genome. additionally, all nanopore data used in this analysis were aligned using bwa, while giab pacbio data were aligned using blasr., to handle the large data volume, the original marginalign and signalalign algorithms were ported to cloud infrastructures using the toil batch system. toil allows for computational resources to be scaled horizontally and vertically as a given […]

PMCID: 4817224
PMID: 26840485
DOI: 10.1038/nature16996

[…] designated as high-quality (due to having more complement events than template events) in the fail folder as determined by poretools were extracted into fasta (for nanopolish) and fastq format (for marginalign) with poretools version 0.5.1 ., we use a reference mapping approach to detect single nucleotide variants through alignment to a reference strain from early in the outbreak (em_079517) . […]

PMCID: 4786906
PMID: 26998227
DOI: 10.12688/f1000research.7229.1

[…] platform (r7.3 pore, version 5 chemistry) the yields of high quality data from the instrument are becoming impressive, with up to several hundreds of megabases per run. using the nanopore-optimised marginalign software they report impressive accuracy scores of 92–93% when considering the filtered, best quality two-direction “passing” data., the marc analysis is as close we have to a hayne’s […]


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marginAlign institution(s)
University of California Santa Cruz Genomics Institute, Santa Cruz, CA, USA; Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
marginAlign funding source(s)
Supported by the National Human Genome Research Institute of the National Institutes of Health under Award Numbers HG006321, HG007827, and U54HG007990.

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