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Nanopore Synthetic-long NaS

A hybrid approach developed to take advantage of data generated using MinION device. We combine Illumina and Oxford Nanopore technologies to produce NaS reads of up to 60 kb that aligned with no error to the reference genome and spanned repetitive regions.

Official website
Specifications
Doc. & support
Credits
Publications
Classification

Specifications

Software type:: Pipeline
Interface:: Command line interface
Restrictions to use:: None
Input data:: Long reads and paired short reads
Output data:: Corrected long reads
Biological technology:: Illumina, Pacific Biosciences, Oxford Nanopore
Operating system:: Unix/Linux
Programming languages:: Perl, Shell (Bash)
License:: CeCILL version 2.1
Computer skills:: Advanced
Version:: NaS version 2
Stability:: Stable
Requirements:: Newbler, blat, last, parallel

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Documentation & support

Maintainer

NaS <nas at genoscope.cns.fr>

Credits

Institution(s)

Commissariat à l’Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France

Publications

(Madoui et al., 2015) Genome assembly using Nanopore-guided long and error-free DNA reads. BMC genomics.
DOI: 10.1186/s12864-015-1519-z

Classification

Literature

(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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