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Identification and correction of systematic error in high-throughput sequence data

Frazer Meacham, Dario Boffelli, Joseph Dhahbi, David IK Martin, Meromit Singer, Lior Pachter
2011 BMC Bioinformatics  
A feature common to all DNA sequencing technologies is the presence of base-call errors in the sequenced reads.  ...  We conclude that correction of systematic errors is important to consider in the design and interpretation of high-throughput sequencing experiments.  ...  A main purpose when designing SysCall was to be able to distinguish systematic errors from heterozygous sites in datasets of lower coverage than that available to us (35.4×).  ... 
doi:10.1186/1471-2105-12-451 pmid:22099972 pmcid:PMC3295828 fatcat:6tp3mqubfjdrbfvejgctr72ddi

Identification and correction of systematic error in high-throughput sequence data

Meromit Singer, Frazer Meacham, Dario Boffelli, Joseph Dhahbi, David Martin, Meromit Singer, Lior Pachter
2011 Nature Precedings  
A feature common to all DNA sequencing technologies is the presence of base-call errors in the sequenced reads.  ...  We conclude that correction of systematic errors is important to consider in the design and interpretation of high-throughput sequencing experiments.  ...  Making use of our characterization we have designed and implemented a classifier to correct for systematic errors at much lower coverage depths.  ... 
doi:10.1038/npre.2011.5989 fatcat:azt5v6r3kff4ffqwdx23nu7m3q

Identification and correction of systematic error in high-throughput sequence data

Meromit Singer, Frazer Meacham, Dario Boffelli, Joseph Dhahbi, David Martin, Meromit Singer, Lior Pachter
2011 Nature Precedings  
A feature common to all DNA sequencing technologies is the presence of base-call errors in the sequenced reads.  ...  We conclude that correction of systematic errors is important to consider in the design and interpretation of high-throughput sequencing experiments.  ...  Making use of our characterization we have designed and implemented a classifier to correct for systematic errors at much lower coverage depths.  ... 
doi:10.1038/npre.2011.5989.1 fatcat:ztzegs4kvnhgtc2dxt23oiq4ka

Spatially Balanced Sampling: Application to Environmental Surveys

J.A. Brown, B.L. Robertson, T. McDonald
2015 Procedia Environmental Sciences  
The process used to select these sites is called the survey design. Spatially balanced designs ensure there is spatial coverage of the entire survey area.  ...  The coverage from GRTS has a stochastic component rather than a fixed interval, regularly spaced coverage as in a systematic sampling design.  ...  One of the earliest designs that aimed for full spatial coverage is two-dimensional systematic sampling.  ... 
doi:10.1016/j.proenv.2015.07.108 fatcat:hqfpsl2kqnbvneemclrtgjsf5a

57 Precision neoantigen discovery using novel algorithms and expanded HLA-ligandome datasets

Dattatreya Mellacheruvu, Rachel Pyke, Charles Abbott, Nick Phillips, Sejal Desai, Rena McClory, John West, Richard Chen, Sean Boyle
2020 Journal for ImmunoTherapy of Cancer  
Our algorithm, named Systematic HLA Epitope Ranking Pan Algorithm (SHERPA™), is integrated into the ImmunoID NeXT Platform®, our immuno-genomics and transcriptomics platform specifically designed to enable  ...  We have extended upon our work by systematically integrating large quantities of high-quality, publicly available data, implementing new modelling algorithms, and rigorously testing our models.  ...  Studies utilizing neoepitope and HLA LOH prediction require careful validation for HLA calls, including assessments of coverage and homozygous rates, and may benefit from increased HLA locus coverage.  ... 
doi:10.1136/jitc-2020-sitc2020.0057 fatcat:zj3dz2jftrbadco2ypkspgutwi

SpecTest: Specification-Based Compiler Testing [chapter]

Richard Schumi, Jun Sun
2021 Lecture Notes in Computer Science  
features.  ...  Compared to existing approaches, SpecTest is built upon a novel test coverage criterion called semantic coverage which brings together mutation testing and fuzzing to specifically target less tested language  ...  First, we design and implement a mutator which systematically introduces less-exercised language features into the test programs automatically.  ... 
doi:10.1007/978-3-030-71500-7_14 fatcat:rjehaw3wtbhozlqkoxjh2kocd4

56 Improved next generation sequencing based class I HLA typing through exome enhancement

Lee McDaniel, Rachel Pyke, Charles Abbott, Gabor Bartha, John West, Richard Chen, Sean Boyle
2020 Journal for ImmunoTherapy of Cancer  
Poor HLA coverage poses the risk of silently mistyping HLA alleles, yielding inaccurate downstream HLA loss of heterozygosity (LOH) detection and neoepitope predictions.MethodsWe designed the ImmunoID  ...  Studies utilizing neoepitope and HLA LOH prediction require careful validation for HLA calls, including assessments of coverage and homozygous rates, and may benefit from increased HLA locus coverage.  ...  Studies utilizing neoepitope and HLA LOH prediction require careful validation for HLA calls, including assessments of coverage and homozygous rates, and may benefit from increased HLA locus coverage.  ... 
doi:10.1136/jitc-2020-sitc2020.0056 fatcat:rxeyydwhr5e4xppjb5jocvrwu4

A systematic study of electronic structure from graphene tographane

Prachi Chandrachud, Bhalchandra S Pujari, Soumyajyoti Haldar, Biplab Sanyal, D G Kanhere
2010 Journal of Physics: Condensed Matter  
By analyzing the electronic structure for eighteen different hydrogen concentrations, we bring out some novel features of this transition.  ...  We also show that a weak ferromagnetic state exists even for a large hydrogen coverage whenever there is a sub-lattice imbalance in presence of odd number of hydrogen atoms.  ...  While graphene is a semi-metal, a recently synthesized hydrogenated graphene called graphane, is an insulator.  ... 
doi:10.1088/0953-8984/22/46/465502 pmid:21403371 fatcat:yjjkx6mmlfazvljyw4ntyj46am

Fast Functional Test Generation Using an SDL Model [chapter]

Robert L. Probert, Alan W. Williams
1999 IFIP Advances in Information and Communication Technology  
This paper reports the results of a successful study undertaken to determine the suitability of CASE tools and formal methods for systematic, rapid generation of functional test cases.  ...  Tau tool set [4] which supports all three of these languages.  ...  By employing the CASE tool coverage analysis features, coverage of all reachable transitions was ensured.  ... 
doi:10.1007/978-0-387-35567-2_19 fatcat:bj3bmugdnzhzxhgmyfxnqre7o4

Towards Model-Driven Testing of a Web Application Generator [chapter]

Luciano Baresi, Piero Fraternali, Massimo Tisi, Sandro Morasca
2005 Lecture Notes in Computer Science  
So far, the impact of conceptual modelling has been evaluated mostly on analysis and design.  ...  This paper addresses its influence on testing, one of the most important and effort-consuming phases, by investigating how the traditional notions of testing carry over to the problem of verifying the  ...  We call this measure rule coverage.  ... 
doi:10.1007/11531371_13 fatcat:asgwu77i55enjc7egn7swwqcka

SeqHBase: a big data toolset for family based sequencing data analysis

Min He, Thomas N Person, Scott J Hebbring, Ethan Heinzen, Zhan Ye, Steven J Schrodi, Elizabeth W McPherson, Simon M Lin, Peggy L Peissig, Murray H Brilliant, Jason O'Rawe, Reid J Robison (+2 others)
2015 Journal of Medical Genetics  
We have chosen this as a design principle, which allows for users to interrogate different sets of variant calls generated for the same sample.  ...  Given the availability of the large pedigree, SeqHBase also used data from other unaffected family members to systematically exclude false positive variant calls.  ... 
doi:10.1136/jmedgenet-2014-102907 pmid:25587064 pmcid:PMC4382803 fatcat:2gqevfu3frag5macnl47avat3u

Designating Spatial Priorities for Marine Biodiversity Conservation in the Coral Triangle

Irawan Asaad, Carolyn J. Lundquist, Mark V. Erdmann, Ruben Van Hooidonk, Mark J. Costello
2018 Frontiers in Marine Science  
By systematically increasing MPA coverage to 10% of the total area of the CT, the average representation of biodiversity features within the MPA system would increase to over 37%.  ...  We utilized the systematic conservation planning software Zonation as a decision-support tool to ensure representation of biodiversity features while balancing selection of protected areas based on the  ...  Maria Beger and Ruben Venegas Li for their insightful input into earlier conceptualizations of this research.  ... 
doi:10.3389/fmars.2018.00400 fatcat:eystkl4albc25abgbvvph3bagq

SNooPer: a machine learning-based method for somatic variant identification from low-pass next-generation sequencing

Jean-François Spinella, Pamela Mehanna, Ramon Vidal, Virginie Saillour, Pauline Cassart, Chantal Richer, Manon Ouimet, Jasmine Healy, Daniel Sinnett
2016 BMC Genomics  
The flexibility of SNooPer's random forest protects against technical bias and systematic errors, and is appealing in that it does not rely on user-defined parameters.  ...  Here, using a real dataset of 40 childhood acute lymphoblastic leukemia patients, we show how the SNooPer algorithm is not affected by low coverage or low VAFs, and can be used to reduce overall sequencing  ...  Design and implementation Design The purpose of SNooPer is to distinguish sequencing errors (false positives -FPs) from actual somatic variants (true positives -TPs) in matched normal-tumor sequencing  ... 
doi:10.1186/s12864-016-3281-2 pmid:27842494 pmcid:PMC5109690 fatcat:3yt2ldernve77nz6bpemjnp3e4

Systematic unit-testing of Ada programs [chapter]

Joachim Wegener, Ines Fey
1997 Lecture Notes in Computer Science  
The classification-tree editor CTE supports the systematic design of functional test cases. The strengths of AdaTEST are the comprehensive support for test execution and coverage analysis.  ...  Hence, a combination of powerful testing tools is necessary to provide systematic and complete test process automation for the examination of Ada programs.  ...  The classification-tree editor CTE supports the systematic design of functional test cases. It is based on the classification-tree method.  ... 
doi:10.1007/3-540-63114-3_7 fatcat:aousc5qcsvhkplz7n7jsr6ioae

Acute Care Surgery Models Worldwide: A Systematic Review

Mats J. L. van der Wee, Gwendolyn van der Wilden, Rigo Hoencamp
2020 World Journal of Surgery  
This systematic review investigated which components are essential in an ACS model and the state of implementation of ACS models worldwide.  ...  The majority consist of a dedicated nontrauma emergency surgical service, with daytime on-site attending coverage (cleared from elective duties), and 24/7 in-house resident coverage.  ...  However, this systematic review is the only one of its scale identifying essential structural features of ACS models across all continents.  ... 
doi:10.1007/s00268-020-05536-9 pmid:32377860 fatcat:gmvhvvyjmnex7py62ehpb25swe
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