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A de novo genome assembler based on the concept of string graphs. The major goal of SGA is to be very memory efficient, which is achieved by using a compressed representation of DNA sequence reads. It calculates per-base error rates, paired-end fragment-size distributions and coverage metrics in the absence of a reference genome. Additionally, SGA estimates characteristics of the sequenced genome, such as repeat content and heterozygosity that are key determinants of assembly difficulty.

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

  • Jared T. Simpson <jared.simpson at oicr.on.ca>

Institution(s)

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom

  • (Simpson, 2014) Exploring Genome Characteristics and Sequence Quality Without a Reference. Bioinformatics.
    PMID: 24443382
  • (Simpson and Durbin, 2012) Efficient de novo assembly of large genomes using compressed data structures. Genome research.
    PMID: 22156294
  • (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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