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OMIC
10989

GenomeABC

A web server for evaluating the performance of genome assemblers. GenomeABC can be used to evaluate the performance of assemblers on real, hypothetical and mutate genomes. (a) Whole genome is shattered into short reads by sequencers, (b) assemblers read these short reads, (c) assemblers reassembled short reads to generate genome/contigs, (d) performance of an assembler is measured by comparing reference/original with assembled genome, (e) performance of assemblers is calculated in term of N50, error rate and coverage.

Specifications

Interface:
Web user interface
Restrictions to use:
None
Programming languages:
Perl
Computer skills:
Basic
Version:
GenomeABC version 1
First release date:
2010-02-10
Stability:
Beta
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Credits

Developer(s)

Shailesh Kumar, Gajendra P.S. Raghava

Institution(s)

Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh-160036, India

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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