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Repetitive motif detection by Assembly of Repetitive K-mers RepARK

A de novo repeat assembly method which avoids potential biases by using abundant k-mers of NGS WGS reads without requiring a reference genome.

Official website
Specifications
Publications
Classification

Specifications

Software type:: Package
Interface:: Command line interface
Restrictions to use:: None
Operating system:: Unix/Linux
Computer skills:: Advanced
Stability:: Stable

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Publications

(Koch et al., 2014) RepARK–de novo creation of repeat libraries from whole-genome NGS reads. Nucleic acids research.
PMID: 24634442

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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