De novo assembly of human genomes with massively parallel short read sequencing.

By Ruiqiang Li, Hong-mei Zhu, Jue Ruan, W. Qian, X. Fang, Zhongbin Shi, Yingrui Li, Shengting Li, Gao Shan, Karsten Kristiansen and 4 more. Genome Research, 2010

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Next-generation massively parallel DNA sequencing technologies provide ultrahigh throughput at a substantially lower unit data cost; however, the data are very short read length sequences, making de novo assembly extremely challenging. Here, we describe a novel method for de novo assembly of large genomes from short read sequences. We successfully assembled both the Asian and African human genome sequences, achieving an N50 contig size of 7.4 and 5.9 kilobases (kb) and scaffold of 446.3 and 61.9 kb, respectively. The development of this de novo short read assembly method creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost-effective way.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/c6e319a023f932d6d2ff8897c2c91e56e872db8e

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Citations in the corpus

Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology (2012, methodology): “Second-generation genome assemblies have been based on shorter read, massively parallel sequencing technologies and De Bruijn graph assembly techniques [12–15] Depending on the dataset quality, polymorphism, and repetitiveness of the target genome, both approaches generate draft genomes with contig ”
Sequence assembly demystified (2013, methodology): “This approach was extended to the assembly of large genomes in the program ABySS 21 and for the first de novo assembly of a mammalian genome entirely using short reads with the program SOAPdenovo 22 .”
Assembling Single-Cell Genomes and Mini-Metagenomes From Chimeric MDA Products (2013, neutral): “In particular, we show that it improves on A5 (Tritt et al., 2012), ABySS ASSEMBLING SINGLE CELL GENOMES AND MINI-METAGENOMES (Simpson et al., 2009), CLC, 1 EULER-SR (Chaisson et al., 2009), Ray (Boisvert et al., 2010), SOAPde-novo (Li et al., 2010), and Velvet (Zerbino and Birney, 2008) in multicel”
Assembly Algorithms for Next-Generation Sequencing Data (2010, positive): “The SOAPdenovo program [59] generated high-quality mammalian genome sequences from billions of Solexa reads of length 75 bp and less [60,61].”
Hybrid error correction and de novo assembly of single-molecule sequencing reads (2012, methodology): “The baseline SOAPdenovo assembly (purple star) represents an assembly of 50× of real 76-bp Illumina paired-end (300 bp) reads from S. cerevisiae S228c.”
GapFiller: a de novo assembly approach to fill the gap within paired reads (2012, background): “Among the most popular ones we mention the Panda genome project [3], the assembly of specific human Individuals [4] (Han Chinese and Yoruban), and several other species [5].”
Metagenomic analysis reveals wastewater treatment plants as hotspots of antibiotic resistance genes and mobile genetic elements. (2017, neutral): “L 90 -u) (Li et al., 2010).”
A human gut microbial gene catalog established by metagenomic sequencing (2010, methodology): “UsingSOAPdenovo 19 ,adeBruijngraph-basedtoolspecially designed for assembling very short reads, we performed de novo assembly for all of the Illumina GA sequence data.”
Insights from 20 years of bacterial genome sequencing (2015, background): “Another approach within an alignment-free category for whole genome and proteome comparison was proposed by Jun and colleagues (Li et al. 2010).”
A survey of sequence alignment algorithms for next-generation sequencing (2010, methodology): “Given a query AGC, for example, the path matching the query is [0, 6]! [3, 3]![5, 5]![1, 1].”
SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler (2012, methodology): “The previous assembly was done using SOAPdenovo1 [3], but in addition it was also limited by the very short read lengths (~35 bp) that were the standard output of Illumina Genome Analyzers (GAIIx) at that time and by the insert sizes available (maximum size is 10 kb).”