articleNucleic Acids ResearchApr 29, 2016GOLD OA

Redundans: an assembly pipeline for highly heterozygous genomes

LPLeszek P. PryszczTGToni Gabaldón

Centre for Genomic Regulation · International Institute of Molecular and Cell Biology · +2 more institutions

PubMed
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Abstract

Many genomes display high levels of heterozygosity (i.e. presence of different alleles at the same loci in homologous chromosomes), being those of hybrid organisms an extreme such case. The assembly of highly heterozygous genomes from short sequencing reads is a challenging task because it is difficult to accurately recover the different haplotypes. When confronted with highly heterozygous genomes, the standard assembly process tends to collapse homozygous regions and reports heterozygous regions in alternative contigs. The boundaries between homozygous and heterozygous regions result in multiple assembly paths that are hard to resolve, which leads to highly fragmented assemblies with a total size larger than…

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Topics & keywords

Topics
Keywords
  • Contig
  • Biology
  • Genome
  • Synteny
  • Genetics
  • Pipeline (software)
  • Loss of heterozygosity
  • Computational biology
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