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RUbioSeq: a suite of parallelized pipelines to automate exome variation and bisulfite-seq analyses

M. Rubio-Camarillo, G. Gomez-Lopez, J. M. Fernandez, A. Valencia, D. G. Pisano
2013 Bioinformatics  
Motivation: RUbioSeq has been developed to facilitate the primary and secondary analysis of re-sequencing projects by providing an integrated software suite of parallelized pipelines to detect exome variants  ...  (single-nucleotide variants and copy number variations) and to perform bisulfite-seq analyses automatically.  ...  Carrillo for experimental validation, technical assistance and fruitful discussions.  ... 
doi:10.1093/bioinformatics/btt203 pmid:23630175 pmcid:PMC3694642 fatcat:fneoupjbfzdijcbvljl4nxmpei

Bis-SNP: Combined DNA methylation and SNP calling for Bisulfite-seq data

Yaping Liu, Kimberly D Siegmund, Peter W Laird, Benjamin P Berman
2012 Genome Biology  
Bisulfite treatment of DNA followed by high-throughput sequencing (Bisulfite-seq) is an important method for studying DNA methylation and epigenetic gene regulation, yet current software tools do not adequately  ...  We have developed a modelbased bisulfite SNP caller, Bis-SNP, that results in substantially better SNP calls than existing methods, thereby improving methylation estimates.  ...  Abbreviations CpG: dinucleotide sequencing consisting of a cytosine followed by guanine; Acknowledgements Support to YL, PWL, and BPB was provided by NIH grant number U24CA143882.  ... 
doi:10.1186/gb-2012-13-7-r61 pmid:22784381 pmcid:PMC3491382 fatcat:faoxp5ti2bdttcm2xk7c7t7e6y

Integrating Epigenomics into the Understanding of Biomedical Insight

Yixing Han, Ximiao He
2016 Bioinformatics and Biology Insights  
Abstr Act: Epigenetics is one of the most rapidly expanding fields in biomedical research, and the popularity of the high-throughput next-generation sequencing (NGS) highlights the accelerating speed of  ...  In this review, we introduce the epigenetics pioneering achievements in health status and complex diseases; next, we give a systematic review of the epigenomics data generation, summarize public resources  ...  161 rmaP A Wild-card bisulfite aligner included in a general-purpose alignment tool http://rulai.cshl.edu/rmap/ 6 segemehl A wild-card bisulfite aligner included in a general-purpose alignment  ... 
doi:10.4137/bbi.s38427 pmid:27980397 pmcid:PMC5138066 fatcat:ne6mu3bdhzhzno5hqjvgmxp3nu

GenPipes: an open-source framework for distributed and scalable genomic analyses

Mathieu Bourgey, Rola Dali, Robert Eveleigh, Kuang Chung Chen, Louis Letourneau, Joel Fillon, Marc Michaud, Maxime Caron, Johanna Sandoval, Francois Lefebvre, Gary Leveque, Eloi Mercier (+11 others)
2019 GigaScience  
With the decreasing cost of sequencing and the rapid developments in genomics technologies and protocols, the need for validated bioinformatics software that enables efficient large-scale data processing  ...  We would also like to acknowledge Romain Gregoire and Tushar Dubey for their contribution to the code and Patricia Goerner-Potvin for her help in planning the report content.  ...  A schema of pipeline steps can be found in Fig. S14 . Comparison with other solutions for next-generation sequencing analysis Data collected for select tools modified from Griffith et al.  ... 
doi:10.1093/gigascience/giz037 pmid:31185495 pmcid:PMC6559338 fatcat:rqn3brcaazajrhmm2boqynaaee

Parallel computing for genome sequence processing

You Zou, Yuejie Zhu, Yaohang Li, Fang-Xiang Wu, Jianxin Wang
2021 Briefings in Bioinformatics  
For each kind of application, its background is firstly introduced, and then a list of tools or algorithms are summarized in the aspects of principle, hardware platform and computing efficiency.  ...  The programming model of each hardware and application provides a reference for researchers to choose high-performance computing tools.  ...  Funding This work is supported in part by the National Natural Science Foundation of China under grants (Nos U1909208, 61732009, 61772557), Hunan Provincial Science and Technology Program (No. 2018WK4001  ... 
doi:10.1093/bib/bbab070 pmid:33822883 fatcat:a4hj2fhybrc6zlsq6xyiu6snmy

An integrated package for bisulfite DNA methylation data analysis with Indel-sensitive mapping

Qiangwei Zhou, Jing-Quan Lim, Wing-Kin Sung, Guoliang Li
2019 BMC Bioinformatics  
Bisulfite sequencing (BS-Seq) is a sequencing approach that provides quantitative cytosine methylation levels in genome-wide scope and single-base resolution.  ...  In addition, a DNA methylation visualization program and a differential analysis program are provided in BatMeth2.  ...  The funding body did not play any role in the study design and collection, analysis and interpretation of the data and the write-up of the manuscript.  ... 
doi:10.1186/s12859-018-2593-4 fatcat:6qbrvh5w6fhgbl2iaqotahbrci

DNA methylation-based forensic age prediction using artificial neural networks and next generation sequencing

Athina Vidaki, David Ballard, Anastasia Aliferi, Thomas H. Miller, Leon P. Barron, Denise Syndercombe Court
2017 Forensic Science International: Genetics  
In an attempt to create a sensitive and accurate age prediction test, a next generation sequencing (NGS)-based method able to quantify the methylation status of the selected 16 CpG sites was developed  ...  In total, 45 age-associated CpG sites were selected based on their reported age coefficients in a previous extensive study and investigated using publicly available methylation data obtained from 1156  ...  The authors would also like to thank the researchers involved in the specific genome-wide DNA methylation studies used here for making their data available, without which this study would not be feasible  ... 
doi:10.1016/j.fsigen.2017.02.009 pmid:28254385 pmcid:PMC5392537 fatcat:vs6yeigcn5cvrbsjp3ffcxmoba

Ecological plant epigenetics: Evidence from model and non-model species, and the way forward

Christina L. Richards, Conchita Alonso, Claude Becker, Oliver Bossdorf, Etienne Bucher, Maria Colomé-Tatché, Walter Durka, Jan Engelhardt, Bence Gaspar, Andreas Gogol-Döring, Ivo Grosse, Thomas P. van Gurp (+14 others)
2017 Ecology Letters  
, the Synthesis Centre of the German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, funded by the German Research Foundation (FZT 118).  ...  ACKNOWLEDGEMENTS This paper is a joint effort of the working group 'sEpiDiv -Towards understanding the causes and consequences of epigenetic diversity' organised by K.H. and L.O., kindly supported by sDiv  ...  Bisulfite sequencing is the gold standard of DNA methylation analysis, as it evaluates individual cytosines in a target sequence or for essentially all cytosines in a genome (i.e. whole-genome bisulfite  ... 
doi:10.1111/ele.12858 pmid:29027325 fatcat:2xsu4a2j4ndfzcxlmnuauplrhe

MethylStar: A fast and robust pre-processing pipeline for bulk or single-cell whole-genome bisulfite sequencing data

Yadollah Shahryary, Rashmi R. Hazarika, Frank Johannes
2020 BMC Genomics  
Whole-Genome Bisulfite Sequencing (WGBS) is a Next Generation Sequencing (NGS) technique for measuring DNA methylation at base resolution.  ...  MethylStar integrates well-established tools for read trimming, alignment and methylation state calling in a highly parallelized environment, manages computational resources and performs automatic error  ...  Acknowledgements We thank Markus List for his suggestion to use a docker container for version control. Authors' contributions FJ, RRH and YS conceptualized the method.  ... 
doi:10.1186/s12864-020-06886-3 pmid:32660416 fatcat:hgs64riav5czfljzdrgpc5zzru

Ecological plant epigenetics: Evidence from model and non-model species, and the way forward [article]

Christina L. Richards, Conchita Alonso, Claude Becker, Oliver Bossdorf, Etienne Bucher, Maria Colome-Tatche, Walter Durka, Jan Engelhardt, Bence Gaspar, Andreas Gogol-Doring, Ivo Grosse, Thomas P. van Gurp (+13 others)
2017 bioRxiv   pre-print
In contrast, studies with model species have benefited from powerful genomic resources, which allow for a more mechanistic understanding but have limited ecological realism.  ...  markers of DNA methylation.  ...  Bisulfite sequencing methods Bisulfite treatment converts unmethylated cytosines to uracil, providing the basis for identifying methylated cytosines upon sequencing and comparing a treated sample to a  ... 
doi:10.1101/130708 fatcat:pzs6p4aakrhorgbrujvi34zy7e

Identification of rare de novo epigenetic variations in congenital disorders

Mafalda Barbosa, Ricky S. Joshi, Paras Garg, Alejandro Martin-Trujillo, Nihir Patel, Bharati Jadhav, Corey T. Watson, William Gibson, Kelsey Chetnik, Chloe Tessereau, Hui Mei, Silvia De Rubeis (+12 others)
2018 Nature Communications  
For each DMR observed in blood, we generated plots of these loci and manually curated for concordance in the other available tissues ( Supplementary Fig. 9 ).  ...  We downloaded from GEO (GSE48472) the methylation profiles generated using the Illumina 450k array from five deceased individuals, each profiled in six different tissues (peripheral blood, liver, skeletal  ...  Primers were designed using MethPrimer, bisulfite-converted DNA was amplified by PCR, followed by next-generation sequencing (NGS) (Illumina MiSeq).  ... 
doi:10.1038/s41467-018-04540-x pmid:29802345 pmcid:PMC5970273 fatcat:kgifmzpqgradvhdz66xzmhswae

PEMapper and PECaller provide a simplified approach to whole-genome sequencing

H. Richard Johnston, Pankaj Chopra, Thomas S. Wingo, Viren Patel, Michael P. Epstein, Jennifer G. Mulle, Stephen T. Warren, Michael E. Zwick, David J. Cutler
2017 Proceedings of the National Academy of Sciences of the United States of America  
Whole-genome sequencing data are fast becoming the most natural dataset for all genetic studies. Analysis tools for data at this scale are essential.  ...  Genome Analysis Toolkit (GATK) in all key measures of performance on human whole-genome sequences. genome sequencing | GATK | sequence mapping | SNP calling | software W hole-genome sequencing (WGS) using  ...  , and the National Center for Research Resources for performing the Illumina sequencing runs.  ... 
doi:10.1073/pnas.1618065114 pmid:28223510 pmcid:PMC5347547 fatcat:7qdqgnjjtveujlcatbqrfsbsoa

Enhancing cancer clonality analysis with integrative genomics

Erich A Peterson, Michael A Bauer, Shweta S Chavan, Cody Ashby, Niels Weinhold, Christoph J Heuck, Gareth J Morgan, Donald J Johann
2015 BMC Bioinformatics  
The seemingly natural capability of cancer to adapt dynamically in a Darwinian manner is a primary reason for therapeutic failures.  ...  Conclusion: The iCloneViz approach can be used for analysis of clonal evolution and mutational dynamics of multi-omic data sets.  ...  The MPMDB provides many other features to facilitate the analysis of complex next generation sequencing (NGS) data, including extensive extract-transform-load (ETL) capabilities for data cleaning as well  ... 
doi:10.1186/1471-2105-16-s13-s7 pmid:26424171 pmcid:PMC4597064 fatcat:oc3d33b47nbbdobt36pn7gemte

PEMapper / PECaller: A simplified approach to whole-genome sequencing [article]

Henry Richard Johnston, Pankaj Chopra, Thomas Wingo, Viren Patel, Michael Epstein, Jennifer Mulle, Stephen Warren, Michael Zwick, David J Cutler
2016 bioRxiv   pre-print
used Genome Analysis Toolkit (GATK) in all key measures of performance on human whole-genome sequences.  ...  In addition to improved computational efficiency, we implement a novel statistical framework that allows for a base-by-base error model, allowing this package to perform as well or better than the widely  ...  ACKNOWLEDGEMENTS 738 We thank members of the Cutler and Zwick labs for comments on the manuscript, Cheryl T. 739  ... 
doi:10.1101/076968 fatcat:z67cmy2pbvfttjffupu6627yfy

Using single-cell multiple omics approaches to resolve tumor heterogeneity

Michael A. Ortega, Olivier Poirion, Xun Zhu, Sijia Huang, Thomas K. Wolfgruber, Robert Sebra, Lana X. Garmire
2017 Clinical and Translational Medicine  
Recent advances in next-generation sequencing and computational biology have utilized single-cell applications to build deep profiles of individual cells that are otherwise masked in bulk profiling.  ...  In addition, the development of new techniques for combining single-cell multi-omic strategies is providing a more precise understanding of factors contributing to cellular identity, function, and growth  ...  Acknowledgements We would like to thank all the members of the Garmire Lab for their helpful discussions and manuscript review.  ... 
doi:10.1186/s40169-017-0177-y pmid:29285690 pmcid:PMC5746494 fatcat:4o55gjckdfdurcrus4ftrldzbu
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