Secure and robust cloud computing for high-throughput forensic microsatellite sequence analysis and databasing

Bailey, Sarah F.; Scheible, Melissa; Williams, Christopher; Silva, Deborah S.B.S.; Hoggan, Marina; Eichman, Christopher; Faith, Seth A.

doi:10.1016/j.fsigen.2017.08.008

Cited by 12 publications

(6 citation statements)

References 23 publications

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“…Once the basic command-line skills are comfortably obtained, the following software can be run just as confidently through a terminal window as clicking an icon in a GUI. While there are a few software options available through web-based interfaces [23][24][25], some developers offer [21,34] or transition to [35] providing a version of their software that can be downloaded as a 'Docker image'. This is a 'ready to use' packet of the program and all its dependencies required to run the application successfully, regardless of the underlying resources available locally [36].…”

Section: Freely Available Softwarementioning

confidence: 99%

“…The software is capable of processing MPS data of a predefined set of STRs (autosomal, X-and Y-STRs) [52,53] generated by different platforms, including the MinION. The analysis is robust and is ready to accommodate batch data processing [25]. The target regions for locus identification parameters are adapted from STRaitRazor v2.0 [12] and locus definitions are collated in a lookup table for the software to identify the targeted loci.…”

Section: Altiusmentioning

confidence: 99%

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An Introductory Overview of Open-Source and Commercial Software Options for the Analysis of Forensic Sequencing Data

Huszar

Gettings

Vallone

2021

Genes

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The top challenges of adopting new methods to forensic DNA analysis in routine laboratories are often the capital investment and the expertise required to implement and validate such methods locally. In the case of next-generation sequencing, in the last decade, several specifically forensic commercial options became available, offering reliable and validated solutions. Despite this, the readily available expertise to analyze, interpret and understand such data is still perceived to be lagging behind. This review gives an introductory overview for the forensic scientists who are at the beginning of their journey with implementing next-generation sequencing locally and because most in the field do not have a bioinformatics background may find it difficult to navigate the new terms and analysis options available. The currently available open-source and commercial software for forensic sequencing data analysis are summarized here to provide an accessible starting point for those fairly new to the forensic application of massively parallel sequencing.

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Section: Freely Available Softwarementioning

confidence: 99%

Section: Altiusmentioning

confidence: 99%

An Introductory Overview of Open-Source and Commercial Software Options for the Analysis of Forensic Sequencing Data

Huszar

Gettings

Vallone

2021

Genes

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“…The main concept of cloud computing is to provide services in real-time according to users' demands by sharing hardware resources and software programs. In recent years, there have been many well-known companies involved in the field of cloud computing, such as Google, IBM, Microsoft, Yahoo, and Amazon [3,4,[10][11][12]. Google, the number one Internet search engine in the US, utilizes the concept of cloud computing a long time ago on its own services, such as Gmail, YouTube, Google Docs, Google Talk, Google Calendar, and Google Gadget, etc.…”

Section: The Cloud Computingmentioning

confidence: 99%

The High Performance of a Task Scheduling Algorithm Using Reference Queues for Cloud- Computing Data Centers

2020

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As the network technology continues to grow at a high rate of speed, the traditional network topology is improved with novel distributed topologies such as the Cloud computing network. A cloud computing environment consists of a huge number of processors and memories, high-speed networks, and various application services to provide a lot of services over the Internet for users. However, many services need to search for suitable service nodes, and the workload of each node can be unbalanced. Based on the reason above, the Reference Queue based Cloud Service Architecture (RQCSA) and Fitness Service Queue Selection Mechanism (FSQSM) are proposed to handle more tasks, lower the makespan and queue waiting time, and improve efficiency. Moreover, the tasks can be distributed more evenly to avoid overloading cluster managers and lower the efficiency of the system.

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“…The raw data (FASTQ files) were processed using the Altius Cloud system [15], which is built upon the Amazon Web Services (AWS) platform. The Altius system identifies target regions in the flanking regions of the STR sequences and produces an output data following the nomenclature guidance of Parson et al [16].…”

Section: Sample Analysis: Bioinformatics Quality Control and Statisticsmentioning

confidence: 99%

Genetic analysis of Southern Brazil subjects using the PowerSeq™ AUTO/Y system for short tandem repeat sequencing

Silva

Sawitzki

Scheible

et al. 2018

Forensic Science International: Genetics

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Secure and robust cloud computing for high-throughput forensic microsatellite sequence analysis and databasing

Cited by 12 publications

References 23 publications

An Introductory Overview of Open-Source and Commercial Software Options for the Analysis of Forensic Sequencing Data

An Introductory Overview of Open-Source and Commercial Software Options for the Analysis of Forensic Sequencing Data

The High Performance of a Task Scheduling Algorithm Using Reference Queues for Cloud- Computing Data Centers

Genetic analysis of Southern Brazil subjects using the PowerSeq™ AUTO/Y system for short tandem repeat sequencing

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