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An open source program and Python library for de novo sequencing, consensus and variant calling on data from Oxford Nanopore Technologies’ MinION platform. Features include: de novo error correction without reference using overlap alignment; reference error correction; scoring known sequence variants on a given dataset; straightforward subdivision of processing for cluster/parallel tasks.

Software type:
Package
Interface:
Command line interface
Restrictions to use:
None
Biological technology:
Oxford Nanopore
Operating system:
Unix/Linux
Programming languages:
Python
Computer skills:
Advanced
Stability:
Stable
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Institution(s)

School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, USA; Department of Physics, Harvard University, Cambridge, Massachusetts, USA

  • (Szalay and Golovchenko, 2015) De novo sequencing and variant calling with nanopores using PoreSeq. Nature biotechnology.
    PMID: 26352647
  • (Magoc et al., 2013) GAGE-B: an evaluation of genome assemblers for bacterial organisms. Bioinformatics.
    PMID: 23665771
  • (Miller et al., 2010) Assembly algorithms for next-generation sequencing data. Genomics.
    PMID: 20211242
  • (Narzisi and Mishra, 2011) Comparing de novo genome assembly: the long and short of it. PloS one.
    PMID: 21559467
  • (Henson et al., 2012) Next-generation sequencing and large genome assemblies. Pharmacogenomics.
    PMID: 22676195
  • (Kleftogiannis et al., 2013) Comparing memory-efficient genome assemblers on stand-alone and cloud infrastructures. PloS one.
    PMID: 24086547
  • (Nagarajan and Pop, 2013) Sequence assembly demystified. Nature reviews Genetics.
    PMID: 23358380
  • (Bradnam et al., 2013) Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. GigaScience.
    PMID: 23870653
  • (Salzberg et al., 2012) GAGE: A critical evaluation of genome assemblies and assembly algorithms. Genome research.
    PMID: 22147368
  • (Utturkar et al., 2014) Evaluation and validation of de novo and hybrid assembly techniques to derive high-quality genome sequences. Bioinformatics.
    PMID: 24930142
  • (Alkan et al., 2011) Limitations of next-generation genome sequence assembly. Nature methods.
    PMID: 21102452
  • (Love et al., 2016) Evaluation of DISCOVAR de novo using a mosquito sample for cost-effective short-read genome assembly. BMC genomics.
    PMID: 26944054

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