Software tools for Oxford Nanopore sequence data

Nature Methods has a nice technology feature on Oxford Nanopore,  MAP program, and the experiences of 1000’s of researchers who were part of Oxford Nanopore’s MAP program.

Among  other interesting things about Nanopore sequencing, it also has a list of software tools developed for analyzing Oxford Nanopore sequence data from minION (in addition to the cloud based minKnow/Metrichor from Oxford Nanopore) . The technology feature has dusted-off a long due post listing the software tools for analyzing Oxford Nanopore data and the papers associated with them. Check out the list below, it has all of the tools mentioned in the Nature Methods article and a few more. Add it if it misses any tool.

poretools: nanopore sequence analysis and visualization software

poRe: tool for analyzing and visualizing nanopore sequence data

nanocorrect: error-correction tool for nanopore sequence data

nanopolish: nanopore sequence analysis and genome assembly software

GraphMap: mapper for long, error-prone reads

LINKS: software to scaffold long reads

nanoCORR: error-correction tool for nanopore sequence data

marginAlign, marginCaller and marginStats: tools to align nanopore reads to a reference genome

MinoTour: real-time analysis tools

NanoOk: Software for pre- and post-alignment analysis of nanopore sequencing data, quality and error profiles

nanopore: variant-detection tool for nanopore sequence data

npReader: real-time conversion and analysis of nanopore reads

  • Software: npReader is available as part of japsa (Just Another JAva Package for Sequence Analysis)

poreSeq: error-correction and variant-calling software for nanopore sequence data

poreMap

poreQC

MinHash: Fast genome and metagenome distance estimation using MinHash

PBcR for  assembly

NaS

You might also be interested in the publications using Oxford Nanopore sequencer.

 

Comments

  1. I was also reminded of NaS at CSHL Genome Informatics last week.

    Genome assembly using Nanopore-guided long and error-free DNA reads
    Paper: http://www.biomedcentral.com/1471-2164/16/327
    Software: http://www.genoscope.cns.fr/externe/nas/

  2. Hi Stephen,
    I think the japsa link is broken. This is the correct one.
    https://github.com/mdcao/japsa
    seb

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