Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads
By Rei Kajitani, Kouta Toshimoto, H. Noguchi, A. Toyoda, Yoshitoshi Ogura, Miki Okuno, Mitsuru Yabana, Masayuki Harada, Eiji Nagayasu, H. Maruyama and 4 more. Genome Research, 2014
988 citations recorded by the source corpus.
Although many de novo genome assembly projects have recently been conducted using high-throughput sequencers, assembling highly heterozygous diploid genomes is a substantial challenge due to the increased complexity of the de Bruijn graph structure predominantly used. To address the increasing demand for sequencing of nonmodel and/or wild-type samples, in most cases inbred lines or fosmid-based hierarchical sequencing methods are used to overcome such problems. However, these methods are costly and time consuming, forfeiting the advantages of massive parallel sequencing. Here, we describe a novel de novo assembler, Platanus, that can effectively manage high-throughput data from heterozygous samples. Platanus assembles DNA fragments (reads) into contigs by constructing de Bruijn graphs with automatically optimized k-mer sizes followed by the scaffolding of contigs based on paired-end information. The complicated graph structures that result from the heterozygosity are simplified during not only the contig assembly step but also the scaffolding step. We evaluated the assembly results on eukaryotic samples with various levels of heterozygosity. Compared with other assemblers, Platanus yields assembly results that have a larger scaffold NG50 length without any accompanying loss of accuracy in both simulated and real data. In addition, Platanus recorded the largest scaffold NG50 values for two of the three low-heterozygosity species used in the de novo assembly contest, Assemblathon 2. Platanus therefore provides a novel and efficient approach for the assembly of gigabase-sized highly heterozygous genomes and is an attractive alternative to the existing assemblers designed for genomes of lower heterozygosity.
Subfields: Molecular Biology, Plant Science
View Paper: https://www.semanticscholar.org/paper/253b71038aa5f03ea12a73771d6a6a987272b05e
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In Molecular Biology
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- Michael C. Schatz
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- Charles J. Underwood
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In Plant Science
Citations in the corpus
- MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization (2019, methodology): “Traditional genome assembly software, for instance, SOAPdenovo2 (22), ALLPATHS-LG (23), Platanus (24), can hardly assemble complete mitogenomes since they are programmed to abandon sequences with extremely-high depth.”
- Contiguous and accurate de novo assembly of metazoan genomes with modest long read coverage (2015, neutral): “That said, some assemblers (Platanus (23) and Falcon (https://github.”
- GenomeScope: Fast reference-free genome profiling from short reads (2016, background): “The profiles reflect the complexity of the genome: homozygous genomes have a simple Poisson profile while heterozygous ones have a characteristic bimodal profile (Kajitani et al. , 2014).”
- Phylogenomics provides a robust topology of the major cnidarian lineages and insights on the origins of key organismal traits (2018, neutral): “Life history stages within Cnidaria are strikingly plastic, making universal definitions difficult [108, 59, 23, 60, 3].”
- Redundans: an assembly pipeline for highly heterozygous genomes (2015, neutral): “1 (10) with default parameters, SOAPdenovo v2.”