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A Review of Bioinformatics Model and Computational Software of Next Generation Sequencing

Jalilah Arijah Mohd Kamarudin, Afnizanfaizal Abdullah, Roselina Sallehuddin
2019 International Journal of Innovative Computing  
These computational software and bioinformatics model are differentiating into three types of bioinformatics analysis stages including alignment, variant calling and filtering and annotation.  ...  In this paper, the description on functionalities, source type and website of the program or software are provided.  ...  VARIANT CALLING After the alignment steps, the next steps in bioinformatics analysis is variant calling. We provide an overview of several of the software package for variant calling in this paper.  ... 
doi:10.11113/ijic.v9n1.217 fatcat:hi3g4qblefgu3ae4vmtjyml6ym

FAVR (Filtering and Annotation of Variants that are Rare): methods to facilitate the analysis of rare germline genetic variants from massively parallel sequencing datasets

Bernard J Pope, Tú Nguyen-Dumont, Fabrice Odefrey, Fleur Hammet, Russell Bell, Kayoko Tao, Sean V Tavtigian, David E Goldgar, Andrew Lonie, Melissa C Southey, Daniel J Park
2013 BMC Bioinformatics  
The principles described herein were applied in our recent publication identifying XRCC2 as a new breast cancer risk gene and have been made publically available as a suite of software tools.  ...  Results: FAVR is a suite of new methods designed to work with commonly used MPS analysis pipelines to assist in the resolution of some of the issues related to the analysis of the vast amount of resulting  ...  Total number of variants found in each individual and observed number of shared variants between first cousins pairs, at the different stages of filtering. N/A indicates non-applicable.  ... 
doi:10.1186/1471-2105-14-65 pmid:23441864 pmcid:PMC3599469 fatcat:e4djtcg3e5hrvci2qyyiyyqkt4

Verification and validation of bioinformatics software without a gold standard: a case study of BWA and Bowtie

Eleni Giannoulatou, Shin-Ho Park, David T Humphreys, Joshua WK Ho
2014 BMC Bioinformatics  
Furthermore, we found that the list of variant calls can be affected unless strict quality control is applied during variant calling.  ...  Bioinformatics software quality assurance is essential in genomic medicine.  ...  This article has been published as part of BMC Bioinformatics Volume 15 Supplement 16, 2014: Thirteenth International Conference on Bioinformatics (InCoB2014): Bioinformatics.  ... 
doi:10.1186/1471-2105-15-s16-s15 pmid:25521810 pmcid:PMC4290646 fatcat:54alhom5ifgnjntqshgmel3lnu

Bioinformatics for Clinical Next Generation Sequencing

G. R. Oliver, S. N. Hart, E. W. Klee
2014 Clinical Chemistry  
Understanding the basic concepts of these analysis steps is important in assessing and addressing the informatics needs of a molecular diagnostics laboratory.  ...  Owing to the complexity of the data, bioinformatics has become a necessary component in any laboratory implementing a clinical NGS test.  ...  However, if NGS software evolves similarly to microarray analysis software, this could become an area of latent focus as software developers strive to improve the initial signal processing in attempts  ... 
doi:10.1373/clinchem.2014.224360 pmid:25451870 fatcat:q2sduxioavformbsn5zoudt5cu

Mendel,MD: a user-friendly online program for clinical exome analysis

Raony Guimarães Corrêa Do Carmo Lisboa Cardenas, Natália Duarte Linhares, Sérgio D Junho Pena
2015 BMC Bioinformatics  
BMC Bioinformatics 2015, 16(Suppl 8):A2  ...  Conclusions Mendel,MD is an efficient, secure and reliable software in exploration of variants from exome data of patients with Mendelian disorders, sophisticated from the bioinformatics perspective and  ...  The bioinformatics challenge is that the software has to be efficient and sophisticated from the computational point-of-view and, at the same time, simple and friendly to be used by clinicians.  ... 
doi:10.1186/1471-2105-16-s8-a2 fatcat:6inelyiwy5brlidc2f7ogzo4qe

Scalability and Validation of Big Data Bioinformatics Software

Andrian Yang, Michael Troup, Joshua W.K. Ho
2017 Computational and Structural Biotechnology Journal  
Validation of software is another important issue in big data bioinformatics that is often ignored.  ...  Determining the correctness of the computational output of big data bioinformatics software is especially difficult due to the large input space and complex algorithms involved.  ...  Acknowledgements This work was supported in part by funds from the New South Wales Ministry of Health, a National Health and Medical Research Council/National Heart Foundation Career Development Fellowship  ... 
doi:10.1016/j.csbj.2017.07.002 pmid:28794828 pmcid:PMC5537105 fatcat:nnkrlwg35fd3hkpbg2jtosdicq

Bioinformatics Pipelines for Targeted Resequencing and Whole-Exome Sequencing of Human and Mouse Genomes: A Virtual Appliance Approach for Instant Deployment

Jason Li, Maria A. Doyle, Isaam Saeed, Stephen Q. Wong, Victoria Mar, David L. Goode, Franco Caramia, Ken Doig, Georgina L. Ryland, Ella R. Thompson, Sally M. Hunter, Saman K. Halgamuge (+7 others)
2014 PLoS ONE  
Despite the rapid development in open source software for analysis of such data, the practical implementation of these tools through construction of sequencing analysis pipelines still remains a challenging  ...  The analyses that are supported in TREVA include: somatic and germline single-nucleotide and insertion/deletion variant calling, copy number analysis, and cohort-based analyses such as pathway and significantly  ...  Acknowledgments NeCTAR (Australia's National eResearch Collaboration Tools and Resources) and Yourgene Bioscience, Taiwan, supported the project with cloud expertise, storage and bandwidth.  ... 
doi:10.1371/journal.pone.0095217 pmid:24752294 pmcid:PMC3994043 fatcat:frixxq25jjdjlcfz6ji6wfvn6e

RVTESTS: an efficient and comprehensive tool for rare variant association analysis using sequence data: Table 1

Xiaowei Zhan, Youna Hu, Bingshan Li, Goncalo R. Abecasis, Dajiang J. Liu
2016 Bioinformatics  
Given the complexity and scale of current sequence datasets and bioinformatics databases, there is a compelling need for more efficient software tools to facilitate these analyses.  ...  To answer this challenge, we developed RVTESTS, which implements a broad set of rare variant association statistics and supports the analysis of autosomal and X-linked variants for both unrelated and related  ...  Efficient software programs for sequence-based association analysis are in great demand.  ... 
doi:10.1093/bioinformatics/btw079 pmid:27153000 pmcid:PMC4848408 fatcat:siliq2a2vjbnpcbk7it75ys7wy

Single-Nucleotide Polymorphism Bioinformatics: A Comprehensive Review of Resources

A. D. Johnson
2009 Circulation: Cardiovascular Genetics  
a bioinformatics analysis of multiple SNPs, an important consideration can be the level of confidence in the true existence of the SNPs of interest.  ...  and the most useful and widely applied markers in genetic studies in the modern age.  ... 
doi:10.1161/circgenetics.109.872010 pmid:20031630 pmcid:PMC2789466 fatcat:hpihw32xhjbapibxxvggljvnum

Novel features and enhancements in BioBin, a tool for the biologically inspired binning and association analysis of rare variants

Anna O Basile, Marta Byrska-Bishop, John Wallace, Alexander T Frase, Marylyn D Ritchie, Oliver Stegle
2017 Bioinformatics  
Motivation: BioBin is an automated bioinformatics tool for the multi-level biological binning of sequence variants.  ...  Herein, we present a significant update to BioBin which expands the software to facilitate a comprehensive rare variant analysis and incorporates novel features and analysis enhancements.  ...  Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btx559 pmid:28968757 pmcid:PMC5860358 fatcat:gjawrr2suzbkfj22ibghggysfq

Planning bioinformatics workflows using an expert system

Xiaoling Chen, Jeffrey T. Chang
2017 Bioinformatics  
In sum, an expert system approach can facilitate exploratory bioinformatic analysis by automating the development of workflows, a task that requires significant domain expertise.  ...  We created the Bioinformatics ExperT SYstem (BETSY) that includes a knowledge base where the capabilities of bioinformatics software is explicitly and formally encoded.  ...  Acknowledgements We thank members of the Chang lab and the UTHealth Bioinformatics Service Center for testing the software. We thank Micheal Hewett for helpful discussions.  ... 
doi:10.1093/bioinformatics/btw817 pmid:28052928 pmcid:PMC5860174 fatcat:zyclakthere5rnrwl44tgelora

Laniakea@ReCaS: exploring the potential of customisable Galaxy on-demand instances as a cloud-based service

Marco Antonio Tangaro, Pietro Mandreoli, Matteo Chiara, Giacinto Donvito, Marica Antonacci, Antonio Parisi, Angelica Bianco, Angelo Romano, Daniela Manila Bianchi, Davide Cangelosi, Paolo Uva, Ivan Molineris (+9 others)
2021 BMC Bioinformatics  
In 2020 we introduced Laniakea, a software platform conceived to streamline the configuration and deployment of "on-demand" Galaxy instances over the cloud.  ...  One of the most successful efforts in improving the availability and usability of bioinformatics tools and data is represented by the Galaxy workflow manager and its thriving community.  ...  Acknowledgements The authors thank ELIXIR-Italy and ReCaS-Bari for providing the computing and bioinformatics facilities.  ... 
doi:10.1186/s12859-021-04401-3 pmid:34749633 pmcid:PMC8574934 fatcat:jszcn3pt4zdxxddlhw7qm5d3su

SVA: software for annotating and visualizing sequenced human genomes

Dongliang Ge, Elizabeth K. Ruzzo, Kevin V. Shianna, Min He, Kimberly Pelak, Erin L. Heinzen, Anna C. Need, Elizabeth T. Cirulli, Jessica M. Maia, Samuel P. Dickson, Mingfu Zhu, Abanish Singh (+2 others)
2011 Bioinformatics  
SVA also provides for flexible interaction with software implementing variant association tests allowing users to consider both the bioinformatic annotation of identified variants and the strength of their  ...  the variants in their genomic contexts.  ...  Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btr317 pmid:21624899 pmcid:PMC3129530 fatcat:mxnm6zj5ezcd3lu7pc5hhmbo2q

GitHub Statistics as a Measure of the Impact of Open-Source Bioinformatics Software

Mikhail G. Dozmorov
2018 Frontiers in Bioengineering and Biotechnology  
We suggest the use of GitHub statistics as an unbiased measure of the usability of bioinformatics software complementing the traditional impact metrics.  ...  , CiteScore) in capturing the level of community attention.  ...  Subject=Bioinformatics limited by the experience of the authors, as well as by a bias to review software published in high-impact journals.  ... 
doi:10.3389/fbioe.2018.00198 pmid:30619845 pmcid:PMC6306043 fatcat:wdppxa7vwjeqnlxdttzwxvymti

A Biosequence-Based Approach to Software Characterization

Christopher S. Oehmen, Elena S. Peterson, Aaron R. Phillips, Darren S. Curtis
2016 2016 IEEE Security and Privacy Workshops (SPW)  
But doing so in a dynamic environment is a nontrivial task because most approaches to software similarity require extensive and time-consuming analysis of a binary, or they fail to recognize executables  ...  Using this method, we show in an example application on large-scale multi-author codes that 1) the biosequence-based method has a statistical performance in recognizing and distinguishing between a collection  ...  ACKNOWLEDGMENT Thanks to Gary Skouson, Dave Cowley, Ping Yang, and Doug Baxter for providing sample executable binaries from the EMSL computing center and for helpful discussions on code differences.  ... 
doi:10.1109/spw.2016.43 dblp:conf/sp/OehmenPPC16 fatcat:4qdkij6p5vdbrpvy4eqpl3ybg4
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