Applied Biosystems SOLiD™ System: Ligation‐Based Sequencing

Pandey, Vicki; Nutter, Robert C.; Prediger, Ellen A.

doi:10.1002/9783527625130.ch3

Cited by 56 publications

(42 citation statements)

References 17 publications

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“…Roche 454 [16] can currently generate reads of <600 bp, and Ion TorrentTM [17] generates read lengths of >200 bp, with longer reads projected in the future. Illumina [18] and ABI SOLiD [19] are short read sequencers with typical read lengths less that 150bp. The second generation sequencing technologies have also developed the capability to read from both ends of a fragment and produce reads with a pair at approximate distance.…”

Section: Related Workmentioning

confidence: 99%

Big data challenges for estimating genome assembler quality

Biswas

Gauthier

Ranjan

et al. 2014

Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics

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The selection of an appropriate assembler is important to obtain best assembly of a fragment dataset, avoid misassembles and minimize further finishing effort. It is known that the assembly quality of assemblers is dependent on the input data parameters such as DNA fragmentation parameters and genome sequence structure. To the best of our knowledge no large scale systematic effort has been made in quantifying the quality of the assembly generated by various assemblers over a range of input parameters. The correlation between input parameters and assembler quality can be used to define the characteristics of an assembler and design an optimal assembler selection algorithm. The critical barrier is the computational challenge of assembling simulated high-throughput sequence libraries of thousands of genomes with input parameters varied to cover the spectrum of values obtained from major sequencers available to biologists today. We present a study to show that a quantifiable correlation can be drawn between their input and output characteristics for four major opensource assemblers. Based on our result we propose a simple model to estimate the quality of assemblies generated by these assemblers for given input parameters.

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Section: Related Workmentioning

confidence: 99%

Big data challenges for estimating genome assembler quality

Biswas

Gauthier

Ranjan

et al. 2014

Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics

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“…In recent years the sequencing technologies have moved from the traditional Sanger Sequencing [2] which produces reads ranging from 750 to 1000 base pairs to the NGS technologies which produce 978-1-4799-0730-4/13/$31.00 ©2013 IEEE shorter reads ranging from 36 to 500 base pairs. Commonly used platforms based on NGS technologies include IlIumina Solexa [1], ABI SOLiD [3] and Roche 454 [4]. The advantages of NGS technologies include lower per base cost at high speeds.…”

Section: Introductionmentioning

confidence: 99%

GAGM: Genome assembly on GPU using mate pairs

Jain¹,

Garg²,

Paul³

2013

20th Annual International Conference on High Performance Computing

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Genome fragment assembl y has long been a time and computation intensive problem in the field of bioinformatics.Man y parallel assemblers have been proposed to accelerate the process but there hasn't been an y effective approach proposed for GPUs. Also with the increasing power of GPUs, applications from various research fields are being parallelized to take advantage of the massive number of "cores" available in GPUs. In this paper we present the design and development of a GPU based assembler (GAGM) for sequence assembl y using Nvidia's GPUs with the CUDA programming model. Our assembler utilizes the mate pair reads produced b y the current NGS technologies to build paired de Bruijn graph. Ever y paired read is broken into paired k-mers and l-mers. Ever y paired k-mer represents a vertex and paired l-mers are mapped as edges. Contigs are formed b y grouping the regions of graph which can be unambiguousl y connected.We present parallel algorithms for k -mer extraction, paired de Bruijn graph construction and grouping of edges. We have benchmarked GAGM on four bacterial genomes. Our results show that the design on GPU is effective in terms of time as well as the qualit y of assembl y produced.

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“…Several short read platforms are now available and seeing rapid adoption in the experimental biology community (454 Life Sciences system [13], Illumina Solexa [1], Applied Biosystems SOLiD [16], and Helicos Biosciences Heliscope [21]). To compensate for the short read lengthwhich makes it difficult to distinguish between overlaps due to genomic co-location, overlaps due to genomic repeats, and overlaps due to random chance -a much higher 100-fold to 300-fold coverage is needed for accurate assembly.…”

Section: Introductionmentioning

confidence: 99%

Parallel de novo assembly of large genomes from high-throughput short reads

Jackson¹,

Regennitter²,

Yang³

et al. 2010

2010 IEEE International Symposium on Parallel &Amp; Distributed Processing (IPDPS)

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The advent of high-throughput short read technology is revolutionizing life sciences by providing an inexpensive way to sequence genomes at high coverage. Exploiting this technology requires the development of a de novo short read assembler, which is an important open problem that is garnering significant research effort. Current methods are largely limited to microbial organisms, whose genomes are two to three orders of magnitude smaller than complex mammalian and plant genomes. In this paper, we present the design and development of a parallel de novo short read assembler that can scale to large genomes with high coverage. Our approach is based on the string graph formulation. Input reads are mapped to short paths, and the genome is reconstructed as a superpath anchored by distance constraints inferred from read pairs. Our method can handle a mixture of multiple read sizes and multiple paired read distances. We present parallel algorithms for string graph construction, string graph compaction, graph based error detection and removal, and computing aggregate summarization of paired read links across graph edges. Using this, we navigate the final graph structure to reproduce large contiguous sequences from the underlying genome. We present a validation of our framework on experimental and simulated data from multiple known genomes and present scaling results on IBM Blue Gene/L.

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Applied Biosystems SOLiD™ System: Ligation‐Based Sequencing

Cited by 56 publications

References 17 publications

Big data challenges for estimating genome assembler quality

Big data challenges for estimating genome assembler quality

GAGM: Genome assembly on GPU using mate pairs

Parallel de novo assembly of large genomes from high-throughput short reads

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