ParDRe: faster parallel duplicated reads removal tool for sequencing studies

González-Domínguez, Jorge; Schmidt, Bertil

doi:10.1093/bioinformatics/btw038

Cited by 38 publications

(43 citation statements)

References 6 publications

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“…Because we observed high rates of likely PCR duplicates among the reads for most samples, the raw reads were de-duplicated using ParDRe (Gonzalez-Dominguez and Schmidt, 2016), allowing one mismatch and using an 18 bp prefix. Testing on internal controls using the ERCC spike-in mix showed that de-duplication improved the correlation of transcript abundances with known relative values (data not shown).…”

Section: Methodsmentioning

confidence: 99%

High Dietary Sugar Reshapes Sweet Taste to Promote Feeding Behavior in Drosophila melanogaster

et al. 2019

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SUMMARY Recent studies find that sugar tastes less intense to humans with obesity, but whether this sensory change is a cause or a consequence of obesity is unclear. To tackle this question, we study the effects of a high sugar diet on sweet taste sensation and feeding behavior in Drosophila melanogaster. On this diet, fruit flies have lower taste responses to sweet stimuli, overconsume food, and develop obesity. Excess dietary sugar, but not obesity or dietary sweetness alone, caused taste deficits and overeating via the cell-autonomous action of the sugar sensor O-linked N-Acetylglucosamine (O-GlcNAc) transferase (OGT) in the sweet-sensing neurons. Correcting taste deficits by manipulating the excitability of the sweet gustatory neurons or the levels of OGT protected animals from diet-induced obesity. Our work demonstrates that the reshaping of sweet taste sensation by excess dietary sugar drives obesity and highlights the role of glucose metabolism in neural activity and behavior.

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Section: Methodsmentioning

confidence: 99%

High Dietary Sugar Reshapes Sweet Taste to Promote Feeding Behavior in Drosophila melanogaster

et al. 2019

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“…(ii) For the removal of duplicate, many strategies are being followed. One of such tools, named ParDRe [5], employs clustering technique for eliminating duplicated reads. It forms groups of reads having similar prefix of length l. Among each group, in parallel, reads are examined for similar suffixes to identify duplicates.…”

Section: Fig 1 Flow Of Ngs Data Processing and Analysismentioning

confidence: 99%

“…This is because the SA is a sorted array having all possible permutations of left rotated sequence of strings. For example, to find the positions where the substring "GA" occurs in the string "GACGAT", the SA interval is found as [4,5]. The SA values with respect to the interval [4,5] are 3 and 0 which are the positions where the substring "GA" is found in the given string.…”

Section: Fig 2 Alignment Of Short Reads Against Reference Genomementioning

confidence: 99%

NGS Short Read Alignment Algorithms and the role of Big Data and Cloud Computing

Rexie¹,

Raimond²,

Mythily³

et al. 2019

IJITEE

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Next Generation Sequencing (NGS) raises opportunities to the computational field for fast and accurate methods for the various challenges associated with NGS data. NGS technology generates a large set of short reads of size 50 to 400 base pairs as a result of biological experiments done on the samples taken from species. Such raw reads are not directly ready for doing most of the analysis or comparative studies to figure out medical related solutions. Hence, the reads have to be assembled to form a complete genome sequence. During the assembly process, there is a high chance of erroneous positioning. Some strategy has to be applied to correct such errors. Once the error-free sequence data is prepared, it is ready for further analysis. The analysis may assist in identifying disease and its cause, similarity check, genetic issue, etc. All of these processes involve data of huge size (in terms of millions per day). To improve the performance of the algorithms working on such vast amount of data, the latest technologies such as Big Data and Cloud Computing can be incorporated. Here, in this paper the evolution of the algorithms for NGS data alignment and the role of Big Data and Cloud Computing technologies are discussed.

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“…Our tool also provides all this functionality (and even more) but in a significantly lower runtime by fully exploiting the parallel processing capabilities of Spark. Although there are a few parallel tools to remove duplicate DNA/RNA sequences (one specific operation that can be used for quality control) on distributed-memory systems [13], [14], up to our knowledge, SeQual is the first publicly available tool intended for this type of parallel systems that provides full functionality (more than 30 operations) instead of only allowing to remove duplicate reads. Furthermore, SeQual includes a graphical user interface intended for simplifying its usage.…”

Section: Introductionmentioning

confidence: 99%

SeQual: Big Data Tool to Perform Quality Control and Data Preprocessing of Large NGS Datasets

2020

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This paper presents SeQual, a scalable tool to efficiently perform quality control of large genomic datasets. Our tool currently supports more than 30 different operations (e.g., filtering, trimming, formatting) that can be applied to DNA/RNA reads in FASTQ/FASTA formats to improve subsequent downstream analyses, while providing a simple and user-friendly graphical interface for non-expert users. Furthermore, SeQual takes full advantage of Big Data technologies to process massive datasets on distributed-memory systems such as clusters by relying on the open-source Apache Spark cluster computing framework. Our scalable Spark-based implementation allows to reduce the runtime from more than three hours to less than 20 minutes when processing a paired-end dataset with 251 million reads per input file on an 8-node multi-core cluster.

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ParDRe: faster parallel duplicated reads removal tool for sequencing studies

Abstract: jgonzalezd@udc.es.

Cited by 38 publications

References 6 publications

High Dietary Sugar Reshapes Sweet Taste to Promote Feeding Behavior in Drosophila melanogaster

High Dietary Sugar Reshapes Sweet Taste to Promote Feeding Behavior in Drosophila melanogaster

NGS Short Read Alignment Algorithms and the role of Big Data and Cloud Computing

SeQual: Big Data Tool to Perform Quality Control and Data Preprocessing of Large NGS Datasets

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