Celera assembler

• Gennady Denisov <>

• (Denisov et al., 2008) Consensus generation and variant detection by Celera Assembler. Bioinformatics.
  PMID: 18321888

J Craig Venter Institute, Chinakville, MD, USA

This work was supported by the J. Craig Venter Institute and by the National Institute of General Medical Sciences (R01 GM077117-01).

Benchmarking

• (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
• (Judge et al., 2016) Comparison of bacterial genome assembly software for MinION data. bioRxiv.
  DOI:  10.1101/049213
• (Chu et al., 2016) Innovations and challenges in detecting long read overlaps: an evaluation of the state-of-the-art. Bioinformatics.
  DOI:  10.1093/bioinformatics/btw811
• (Abbas et al., 2014)  Assessment of de novo assemblers for draft genomes: a case study with fungal genomes. BMC Genomics.
  PMID:  25521762
• (Zhang et al., 2011)  A practical comparison of de novo genome assembly software tools for next-generation sequencing technologies. PLoS One.
  PMID:  21423806

Review of tools

• (Bao et al., 2011)  Evaluation of next-generation sequencing software in mapping and assembly. J Hum Genet.
  PMID:  21525877

Methodology

• (Simpson and Pop, 2015)  The Theory and Practice of Genome Sequence Assembly. Annual review of genomics and human genetics.
  PMID:  25939056