Redundans: an assembly pipeline for highly heterozygous genomes
By Leszek P. Pryszcz, Toni Gabaldón. Nucleic Acids Research, 2015
452 citations recorded by the source corpus.
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 expected. This, in turn, causes numerous problems in downstream analyses such as fragmented gene models, wrong gene copy number, or broken synteny. To circumvent these caveats we have developed a pipeline that specifically deals with the assembly of heterozygous genomes by introducing a step to recognise and selectively remove alternative heterozygous contigs. We tested our pipeline on simulated and naturally-occurring heterozygous genomes and compared its accuracy to other existing tools. Our method is freely available at https://github.com/Gabaldonlab/redundans.
Subfields: Molecular Biology, Plant Science
View Paper: https://www.semanticscholar.org/paper/1471074058fc2ca0ee1bf4d6ae21f3161c16366c
Citations in the corpus
- Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies (2018, unknown): “The HaploMerger2 toolkit [14] and Redundans assembly pipeline [15] were designed to produce haplotype-fused assemblies from short-read sequences.”
- MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization (2019, unknown): “Plus, the heterozygosity rate works against the genome assembly quality using HTS platforms (55).”
- Identifying and removing haplotypic duplication in primary genome assemblies (2019, unknown): “Tools such as Purge_haplotigs (Roach et al., 2018), Haplomerger (Huang et al., 2012), and the Redundans pipeline (Pryszcz and Gabaldón, 2016) have been designed to resolve this problem.”