Assembling millions of short DNA sequences using SSAKE

By René L. Warren, Granger G. Sutton, Steven J. M. Jones, R. Holt. Bioinform., 2006

546 citations recorded by the source corpus.

Abstract Summary: Novel DNA sequencing technologies with the potential for up to three orders magnitude more sequence throughput than conventional Sanger sequencing are emerging. The instrument now available from Solexa Ltd, produces millions of short DNA sequences of 25 nt each. Due to ubiquitous repeats in large genomes and the inability of short sequences to uniquely and unambiguously characterize them, the short read length limits applicability for de novo sequencing. However, given the sequencing depth and the throughput of this instrument, stringent assembly of highly identical sequences can be achieved. We describe SSAKE, a tool for aggressively assembling millions of short nucleotide sequences by progressively searching through a prefix tree for the longest possible overlap between any two sequences. SSAKE is designed to help leverage the information from short sequence reads by stringently assembling them into contiguous sequences that can be used to characterize novel sequencing targets. Availability: Contact: rwarren@bcgsc.ca

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/dbb41f80dc43d139761a863eb7d6da773a726261

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Citations in the corpus

NOVOPlasty: de novo assembly of organelle genomes from whole genome data. (2016, methodology): “To detect these putative variances between our data set and the used reference, we realigned all reads to each assembly with bowtie2 (12) for visual inspection with Tablet (13).”
NOVOPlasty: de novo assembly of organelle genomes from whole genome data (2016, methodology): “To detect these putative variances between our data set and the used reference, we realigned all reads to each assembly with bowtie2 (12) for visual inspection with Tablet (13).”
ABySS: a parallel assembler for short read sequence data. (2009, background): “6 Pevzner 2008), SSAKE (Warren et al. 2007) and EDENA (Hernandez et al.”
Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma. (2012, methodology): “This aggressive filter yielded ;32 million total reads, including 4.5 million paired and 22.9 million unpaired reads, and assembled with SSAKE (v3.”
Velvet: algorithms for de novo short read assembly using de Bruijn graphs. (2008, methodology): “More recently, programs such as SSAKE (Warren et al. 2007), SHARCGS (Dohm et al. 2007), and VCAKE (Jeck et al. 2007) implicitly use this framework, but at a local level.”
De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer. (2008, background): “However, since the required overlapping length represents a significant part of the read length, the effective coverage depth (Lander and Waterman 1988; Wendl and Waterston 2002) provides a more informative value.”
Next-generation DNA sequencing (2008, methodology): “Several assembly tools have recently been adapted or independently developed for generating assemblies from short, unpaired sequencing reads 38–40 .”
Next-generation sequencing: from basic research to diagnostics. (2009, background): “A case in point is a modeling study that indicated that 97% of the E. coli genome can be uniquelyalignedwith18-bpreadsbutthatonly90%of thehumangenomecanbeuniquelyalignedwith30-bp reads (68, 69 ).”
Ray: Simultaneous Assembly of Reads from a Mix of High-Throughput Sequencing Technologies (2010, background): “Over the course of this evolution, a number of algorithmic pathways were followed and quickly rendered obsolete by the sheer volume outputted by the new parallel sequencing technologies.”
Phylogenomic analyses of species relationships in the genus Sabal (Arecaceae) using targeted sequence capture (2016, methodology): “The Velvet contigs were assembled using a hash size of 31, as determined by VelvetOptimiser (Gladman & Seemann, 2012), and were further extended into intron sequence using SSAKE (Warren et al., 2007).”
An Integrated Pipeline for de Novo Assembly of Microbial Genomes (2012, methodology): “These include tools for base calling of the images from the sequencer [1,2], error correction of the sequence reads [3,4], removal of adapter sequence contamination [5], contig assembly [6,7], and scaffolding [8–10].”
Utilization of next-generation sequencing platforms in plant genomics and genetic variant discovery (2010, methodology): “A variety of tools that are beyond the scope of this paper have been developed for alignment and de novo assembly of short reads (for examples, see Warren et al. 2007; Dohm et al. 2007; Jeck et al. 2007 ;D e Bona et al. 2008; Chaisson and Pevzner 2008 ;L i et al. 2008a; Smith et al. 2008; Zerbino ”
Short read fragment assembly of bacterial genomes. (2008, background): “As a result, while assembly of Solexa-sized simulated reads was analyzed in Warren et al. (2007), the assembly of real Solexa reads proved to be more challenging .”
SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing. (2007, methodology): “Comparative evaluation of SHARCGS Warren et al. (2007) recently presented SSAKE, an algorithm to be used for assembling short-read sequences.”
Bioinformatics challenges of new sequencing technology. (2008, methodology): “SSAKE [ 22 ], VCAKE [23] and SHARCGS [24] all use a similar ‘greedy’ approach to genome assembly.”