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Resource: HaploMerger: Reconstructing allelic relationships for polymorphic diploid genome assemblies
- Shengfeng Huang,
- Zelin Chen,
- Guangrui Huang,
- Ting Yu,
- Ping Yang,
- Jie Li,
- Yonggui Fu,
- Shaochun Yuan,
- Shangwu Chen,
- and Anlong Xu
Genome Res. August 2012 22: 1581-1588; Published in Advance May 3, 2012, doi:10.1101/gr.133652.111
...excellent performance without inducing new assembly errors. When applied to three real polymorphic diploid assemblies, HaploMerger gave comparable or better results than manual curation. The first two real assemblies are from Ciona savignyi and Branchiostoma floridae, both of which were generated from...
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RESOURCE: The C. savignyi genetic map and its integration with the reference sequence facilitates insights into chordate genome evolution
- Matthew M. Hill,
- Karl W. Broman,
- Elia Stupka,
- William C. Smith,
- Di Jiang,
- and Arend Sidow
Genome Res. August 2008 18: 1369-1379; Published in Advance June 2, 2008, doi:10.1101/gr.078576.108
.... Eighty-three percent of the reference genome sequence is covered. The chromosomal reconstruction allowed us to investigate the evolution of genome structure in highly polymorphic species, by comparing the genome of C. savignyi to its divergent sister species, Ciona intestinalis . Both genomes have...
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Resource: Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads
- Rei Kajitani,
- Kouta Toshimoto,
- Hideki Noguchi,
- Atsushi Toyoda,
- Yoshitoshi Ogura,
- Miki Okuno,
- Mitsuru Yabana,
- Masayuki Harada,
- Eiji Nagayasu,
- Haruhiko Maruyama,
- Yuji Kohara,
- Asao Fujiyama,
- Tetsuya Hayashi,
- and Takehiko Itoh
Genome Res. August 2014 24: 1384-1395; Published in Advance April 22, 2014, doi:10.1101/gr.170720.113
...obstacles remain in applying de Bruijn-graph-based assembly to the data from massively parallel sequencers. One of the primary difficulties to overcome is the existence of heterozygosity between diploid chromosomes (Vinson et al. 2005; Velasco et al. 2007; The Potato Genome Sequencing Consortium 2011; Star...
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Methods: Detecting heterozygosity in shotgun genome assemblies: Lessons from obligately outcrossing nematodes
- Antoine Barrière,
- Shiaw-Pyng Yang,
- Elizabeth Pekarek,
- Cristel G. Thomas,
- Eric S. Haag,
- and Ilya Ruvinsky
Genome Res. March 2009 19: 470-480; Published in Advance February 9, 2009, doi:10.1101/gr.081851.108
...for species with haploid or nearly homozygous diploid s with relatively few repetitive sequences. Indeed the first s sequenced using the WGS approach contained little heterozygosity because they were derived from highly inbred laboratory strains (e.g., mouse [ Mouse Genome Sequencing Consortium 2002...
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Methods: An MCMC algorithm for haplotype assembly from whole-genome sequence data
- Vikas Bansal,
- Aaron L. Halpern,
- Nelson Axelrod,
- and Vineet Bafna
Genome Res. August 2008 18: 1336-1346; doi:10.1101/gr.077065.108
...sampling approach and joining these local haplotypes using overlaps. This method has recently been extended ( Kim et al. 2007 ) to include polymorphism detection as part of the haplotype reconstruction pipeline, and applied to the of Ciona intestinalis. Recently, Levy et al. (2007) sequenced the complete...
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Method: metaSPAdes: a new versatile metagenomic assembler
- Sergey Nurk,
- Dmitry Meleshko,
- Anton Korobeynikov,
- and Pavel A. Pevzner
Genome Res. May 2017 27: 824-834; Published in Advance March 15, 2017, doi:10.1101/gr.213959.116
...resolve genomic repeats by combining multiple libraries sequenced with various technologies. Lastly, dipSPAdes (Safonova et al. 2015) was developed to address the challenge of assembling a two-haplome mixture within a highly polymorphic diploid . While these recently developed SPAdes tools address...

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