Fast and accurate read alignment for resequencing

Mu, John C.; Jiang, Hui; Kiani, Amirhossein; Mohiyuddin, Marghoob; Asadi, Narges Bani; Wong, Wing Hung

doi:10.1093/bioinformatics/bts450

Cited by 48 publications

(39 citation statements)

References 18 publications

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“…The resulting clean reads no shorter than 75 bp were used for downstream analyses. SeqAlto (version 0.5) was used to align the clean reads of each sample to the reference genome (NC_002937) of D. vulgaris (27). Cufflinks (version 2.2.1) was used to calculate the strand-specific coverage for each gene and to analyze the differential expression on triplicate cultures (28).…”

Section: Methodsmentioning

confidence: 99%

Antimicrobial Effects of Free Nitrous Acid on Desulfovibrio vulgaris: Implications for Sulfide-Induced Corrosion of Concrete

Gao

Lü

et al. 2016

Appl Environ Microbiol

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Hydrogen sulfide produced by sulfate-reducing bacteria (SRB) in sewers causes odor problems and asset deterioration due to the sulfide-induced concrete corrosion. Free nitrous acid (FNA) was recently demonstrated as a promising antimicrobial agent to alleviate hydrogen sulfide production in sewers. However, details of the antimicrobial mechanisms of FNA are largely unknown. Here, we report the multiple-targeted antimicrobial effects of FNA on the SRB Desulfovibrio vulgaris Hildenborough by determining the growth, physiological, and gene expression responses to FNA exposure. The activities of growth, respiration, and ATP generation were inhibited when exposed to FNA. These changes were reflected in the transcript levels detected during exposure. The removal of FNA was evident by nitrite reduction that likely involved nitrite reductase and the poorly characterized hybrid cluster protein, and the genes coding for these proteins were highly expressed. During FNA exposure, lowered ribosome activity and protein production were detected. Additionally, conditions within the cells were more oxidizing, and there was evidence of oxidative stress. Based on an interpretation of the measured responses, we present a model depicting the antimicrobial effects of FNA on D. vulgaris. These findings provide new insight for understanding the responses of D. vulgaris to FNA and will provide a foundation for optimal application of this antimicrobial agent for improved control of sewer corrosion and odor management. S ulfate-reducing bacteria (SRB) are anaerobic chemoorganotrophic microorganisms that typically use sulfate as the terminal electron acceptor for respiration and generate energy with the production of hydrogen sulfide (2). In confined spaces, the production of hydrogen sulfide can cause odor and corrosion problems. This is particularly the case in sewers and inlet structures of wastewater treatment plants, where the oxidation of sulfide produces sulfuric acid, which corrodes the concrete surfaces of the sewer. This results in serious deterioration of sewer assets that requires very costly and demanding rehabilitation efforts (3, 4). Consequently, there is great interest in the efficient control of SRB and thereby minimizing hydrogen sulfide production in sewers.Various chemical dosing methods are used to lower hydrogen sulfide production in sewers, and four strategies currently used include sulfide oxidation by the injection of chemical oxidants, such as air, oxygen, or nitrate (5, 6); sulfide precipitation by addition of iron salts (7); application of magnesium hydroxide or lime to raise the wastewater pH and prevent the release of hydrogen sulfide (8); and inhibition of the activities of SRB to lessen the generation of hydrogen sulfide (9). However, to obtain the required sulfide control, these strategies require continuous chemical consumption and considerable operational costs (10).Free nitrous acid (FNA), the protonated form of nitrite, was recently demonstrated to be the true metabolic inhibitor behind the usu...

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Section: Methodsmentioning

confidence: 99%

Antimicrobial Effects of Free Nitrous Acid on Desulfovibrio vulgaris: Implications for Sulfide-Induced Corrosion of Concrete

Gao

Lü

et al. 2016

Appl Environ Microbiol

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“…SeqAlto [8], CUSHAW2 [9], and GEM [10] were published recently. SeqAlto is a hash-based aligner that improves an earlier hash-based aligner SNAP [11] (reported to have relatively poor sensitivity for real reads and provide no mapping quality [8]) using additional global and local alignments.…”

Section: Introductionmentioning

confidence: 99%

SOAP3-dp: Fast, Accurate and Sensitive GPU-Based Short Read Aligner

et al. 2013

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To tackle the exponentially increasing throughput of Next-Generation Sequencing (NGS), most of the existing short-read aligners can be configured to favor speed in trade of accuracy and sensitivity. SOAP3-dp, through leveraging the computational power of both CPU and GPU with optimized algorithms, delivers high speed and sensitivity simultaneously. Compared with widely adopted aligners including BWA, Bowtie2, SeqAlto, CUSHAW2, GEM and GPU-based aligners BarraCUDA and CUSHAW, SOAP3-dp was found to be two to tens of times faster, while maintaining the highest sensitivity and lowest false discovery rate (FDR) on Illumina reads with different lengths. Transcending its predecessor SOAP3, which does not allow gapped alignment, SOAP3-dp by default tolerates alignment similarity as low as 60%. Real data evaluation using human genome demonstrates SOAP3-dp's power to enable more authentic variants and longer Indels to be discovered. Fosmid sequencing shows a 9.1% FDR on newly discovered deletions. SOAP3-dp natively supports BAM file format and provides the same scoring scheme as BWA, which enables it to be integrated into existing analysis pipelines. SOAP3-dp has been deployed on Amazon-EC2, NIH-Biowulf and Tianhe-1A.

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“…We compare ARYANA with other aligners: Bowtie2 [45], BWA-SW [43], and SeqAlto [30]. ARYANA is multiple times faster than all of these aligners with comparable generality and accuracy.…”

Section: Introductionmentioning

confidence: 99%

ARYANA: Aligning Reads by Yet Another Approach

et al. 2014

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MotivationAlthough there are many different algorithms and software tools for aligning sequencing reads, fast gapped sequence search is far from solved. Strong interest in fast alignment is best reflected in the $106 prize for the Innocentive competition on aligning a collection of reads to a given database of reference genomes. In addition, de novo assembly of next-generation sequencing long reads requires fast overlap-layout-concensus algorithms which depend on fast and accurate alignment.ContributionWe introduce ARYANA, a fast gapped read aligner, developed on the base of BWA indexing infrastructure with a completely new alignment engine that makes it significantly faster than three other aligners: Bowtie2, BWA and SeqAlto, with comparable generality and accuracy. Instead of the time-consuming backtracking procedures for handling mismatches, ARYANA comes with the seed-and-extend algorithmic framework and a significantly improved efficiency by integrating novel algorithmic techniques including dynamic seed selection, bidirectional seed extension, reset-free hash tables, and gap-filling dynamic programming. As the read length increases ARYANA's superiority in terms of speed and alignment rate becomes more evident. This is in perfect harmony with the read length trend as the sequencing technologies evolve. The algorithmic platform of ARYANA makes it easy to develop mission-specific aligners for other applications using ARYANA engine.AvailabilityARYANA with complete source code can be obtained from http://github.com/aryana-aligner

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Fast and accurate read alignment for resequencing

Abstract: whwong@stanford.edu.

Cited by 48 publications

References 18 publications

Antimicrobial Effects of Free Nitrous Acid on Desulfovibrio vulgaris: Implications for Sulfide-Induced Corrosion of Concrete

Antimicrobial Effects of Free Nitrous Acid on Desulfovibrio vulgaris: Implications for Sulfide-Induced Corrosion of Concrete

SOAP3-dp: Fast, Accurate and Sensitive GPU-Based Short Read Aligner

ARYANA: Aligning Reads by Yet Another Approach

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