High-quality draft assemblies of mammalian genomes from massively parallel sequence data

By S. Gnerre, Iain MacCallum, Dariusz Przybylski, Filipe J. Ribeiro, Joshua N. Burton, B. J. Walker, Ted Sharpe, Giles Hall, Terrance Shea, S. Sykes and 10 more. Proceedings of the National Academy of Sciences of the United States of America, 2010

1,617 citations recorded by the source corpus.

Massively parallel DNA sequencing technologies are revolutionizing genomics by making it possible to generate billions of relatively short (~100-base) sequence reads at very low cost. Whereas such data can be readily used for a wide range of biomedical applications, it has proven difficult to use them to generate high-quality de novo genome assemblies of large, repeat-rich vertebrate genomes. To date, the genome assemblies generated from such data have fallen far short of those obtained with the older (but much more expensive) capillary-based sequencing approach. Here, we report the development of an algorithm for genome assembly, ALLPATHS-LG, and its application to massively parallel DNA sequence data from the human and mouse genomes, generated on the Illumina platform. The resulting draft genome assemblies have good accuracy, short-range contiguity, long-range connectivity, and coverage of the genome. In particular, the base accuracy is high (≥99.95%) and the scaffold sizes (N50 size = 11.5 Mb for human and 7.2 Mb for mouse) approach those obtained with capillary-based sequencing. The combination of improved sequencing technology and improved computational methods should now make it possible to increase dramatically the de novo sequencing of large genomes. The ALLPATHS-LG program is available at http://www.broadinstitute.org/science/programs/genome-biology/crd.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/1ac8434e3720941f5ebc1cba517cb757ef79b642

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Citations in the corpus

ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter (2016, neutral): “In addition to the aforementioned assemblers, we also attempted to include ALLPATHS-LG 52488 (Gnerre et al. 2010) and MaSuRCA 3.”
Musket: a multistage k-mer spectrum-based error corrector for Illumina sequence data (2013, methodology): “Corresponding assemblers include Velvet (Zerbino and Birney, 2008), ALLPATHS (Butler et al. , 2008), ABySS (Simpson et al. , 2009), ALLPATHS-LG (Gnerre et al. , 2010), SOAPdenovo (Li et al ., 2010b) and PASHA (Liu et al. , 2011b).”
Experimental and analytical tools for studying the human microbiome (2011, background): “58 ; future applications could leverage the longer reads from the PacBio RS platform); or obtaining long-range connectivity using jumping libraries”
Improving PacBio Long Read Accuracy by Short Read Alignment (2012, background): “Some researchers have been attempting to combine PacBio long reads and SGS short reads, for example the genome assembler Allpaths-LG [5].”
Repetitive DNA and next-generation sequencing: computational challenges and solutions (2011, background): “In response to this influx of new laboratory methods, many novel computational tools have been developed to map NGS reads to genomes and to reconstruct genomes and transcriptome”
Field guide to next‐generation DNA sequencers (2011, background): “2011 Blackwell Publishing Ltd and sample tagging has been clear for several years, during which time a variety of schemes have been developed (e.g. Binladen et al. 2007; Hoffmann et al. 2007; Meyer et al. 2007; Craig et al. 2008).”
De novo assembly and genotyping of variants using colored de Bruijn graphs (2012, methodology): “However, there are established algorithms for using read-pair information to disam-biguate de Bruijn graphs 30,31,39,40,49,50 .”
Integrating Hi-C links with assembly graphs for chromosome-scale assembly (2018, background): “Scaffolding utilizes long-range linking information such as BAC or fosmid clones (Venter et al. , 1996; Gnerre et al. , 2011), optical maps (Schwartz et al. , 1993; Dong et al. , 2013; Shelton et al. , 2015), linked reads (Zheng et al. , 2016; Weisenfeld et al. , 2017; Yeo et al. , 2017), or…”
Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement (2014, methodology): “All draft assemblies were generated using ALLPATHS-LG [41].”
The MaSuRCA genome assembler (2013, methodology): “The original GAGE assembly comparison (Salzberg et al., 2012) compared the following assembly programs: ABySS (Simpson et al., 2009) ALLPATHS-LG (Gnerre et al., 2011) 2671 The MaSuRCA genome assembler Bambus2 (Koren et al., 2011) CABOG (Miller et al., 2008) MSR-CA (now renamed MaSuRCA 1.0) SGA…”
Efficient de novo assembly of large genomes using compressed data structures. (2012, background): “Currently available assemblers require either a single computer with very large amounts of memory—typically in the hundreds of gigabytes (Li et al. 2010b; Gnerre et al. 2011)—or a large distributed cluster of tightly coupled computers (Simpson et al. 2009; Boisvert et al. 2010).”