ArticlePloS one2015
Leveraging the power of high performance computing for next generation sequencing data analysis: tricks and twists from a high throughput exome workflow.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers, 1 of them a synthesis that pooled it.
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
22 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Pooled it
- CEP162 deficiency causes human retinal degeneration and reveals a dual role in ciliogenesis and neurogenesis.The Journal of clinical investigation · 2023Article
- Whole-exome sequencing identified mutational profiles of urothelial carcinoma post kidney transplantation.Journal of translational medicine · 2022Article
- Revealing protein-protein interactions at the transcriptome scale by sequencing.Molecular cell · 2021Article
- Ten simple rules for getting started with command-line bioinformatics.PLoS computational biology · 2021Article
- A rather dry subject; investigating the study of arid-associated microbial communities.Environmental microbiome · 2020Review
- The clinical-phenotype continuum in DYNC1H1-related disorders-genomic profiling and proposal for a novel classification.Journal of human genetics · 2020Article
- The genomic and clinical landscape of fetal akinesia.Genetics in medicine : official journal of the American College of Medical Genetics · 2020Article
- Human exome and mouse embryonic expression data implicate ZFHX3, TRPS1, and CHD7 in human esophageal atresia.PloS one · 2020Article
- QUARTIC: QUick pArallel algoRithms for high-Throughput sequencIng data proCessing.F1000Research · 2020Article
- Novel mutations inCold Spring Harbor molecular case studies · 2019Article
- Review of applications of high-throughput sequencing in personalized medicine: barriers and facilitators of future progress in research and clinical application.Briefings in bioinformatics · 2019Review
- iRODS metadata management for a cancer genome analysis workflow.BMC bioinformatics · 2019Article
- Managing genomic variant calling workflows with Swift/T.PloS one · 2019Article
- Late diagnosis of a truncatingCold Spring Harbor molecular case studies · 2018Article
- Article
- Accelerating next generation sequencing data analysis with system level optimizations.Scientific reports · 2017Article
- Hypomorphic mutations in POLR3A are a frequent cause of sporadic and recessive spastic ataxia.Brain : a journal of neurology · 2017Article
- A deep intronic CLRN1 (USH3A) founder mutation generates an aberrant exon and underlies severe Usher syndrome on the Arabian Peninsula.Scientific reports · 2017Article
- From Wet-Lab to Variations: Concordance and Speed of Bioinformatics Pipelines for Whole Genome and Whole Exome Sequencing.Human mutation · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Next generation sequencing (NGS) has been a great success and is now a standard method of research in the life sciences. With this technology, dozens of whole genomes or hundreds of exomes can be sequenced in rather short time, producing huge amounts of data. Complex bioinformatics analyses are required to turn these data into scientific findings. In order to run these analyses fast, automated workflows implemented on high performance computers are state of the art. While providing sufficient compute power and storage to meet the NGS data challenge, high performance computing (HPC) systems require special care when utilized for high throughput processing. This is especially true if the HPC system is shared by different users. Here, stability, robustness and maintainability are as important for automated workflows as speed and throughput. To achieve all of these aims, dedicated solutions have to be developed. In this paper, we present the tricks and twists that we utilized in the implementation of our exome data processing workflow. It may serve as a guideline for other high throughput data analysis projects using a similar infrastructure. The code implementing our solutions is provided in the supporting information files.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.