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SEME: A Fast Mapper of Illumina Sequencing Reads with Statistical Evaluation

Shijian Chen, Anqi Wang, Lei M. Li
2013 Journal of Computational Biology  
In this report, we make some efforts to evaluate the accuracy of the SEME procedure. In concert with the algorithm, we start off by comparing two sequences of the same read length.  ...  Now the Illumina platform can generate reads longer than 100 bp with fairly high quality. MiSeq (MiSeq Personal Sequencer -Illumina) can even sequence reads up to 250 bp.  ...  This work was supported by the National Center for Mathematics and Interdisciplinary Sciences, Chinese Academy of Sciences (CAS); the Program of ''One hundred talented people,'' CAS; and grant 91130008  ... 
doi:10.1089/cmb.2013.0111 pmid:24195707 pmcid:PMC3822393 fatcat:kb5wlyrs3bckbdts467trevnum

SEME: A Fast Mapper of Illumina Sequencing Reads with Statistical Evaluation [chapter]

Shijian Chen, Anqi Wang, Lei M. Li
2013 Lecture Notes in Computer Science  
In recent years, the sequencing reads of the Illumina platform get longer and their quality scores get higher.  ...  Based on these observations, we propose a fast mapping approach, referred to as "SEME", which has two core steps: first it scans a read sequentially in a specific order for a k-mer exact match seed; next  ...  This work was supported by the National Center for Mathematics and Interdisciplinary Sciences, CAS, the Program of "One hundred talented people", CAS, and grant 91130008 from Chinese National Science Foundation  ... 
doi:10.1007/978-3-642-37195-0_2 fatcat:b534f377nfhipaerrycnkoobim

Novel Computational Techniques For Mapping And Classifying Next-Generation Sequencing Data

Karel Břinda, Gregory Kucherov, Valentina Boeva
2016 Zenodo  
In this thesis, we present novel computational techniques for read mapping and taxonomic classification. With more than a hundred of published mappers, read mapping might be considered fully solved.  ...  An important component of a dynamic mapper is an online consensus caller, i.e., a program collecting alignment statistics and guiding updates of the reference in the online fashion.  ...  MiSeq is a merge of Illumina reads of 10 bacterial genomes, and HMPtongue is a random sample of real Illumina wholemetagenome sequences.  ... 
doi:10.5281/zenodo.1045317 fatcat:agbwpocisncwvihn2ij5q3ongq

Short Read Mapping: An Algorithmic Tour

Stefan Canzar, Steven L. Salzberg
2017 Proceedings of the IEEE  
The first sequencers from Solexa (later Illumina) were able to generate, in a single run, tens of millions of very short DNA sequences, or "reads."  ...  The Short Read Mapping Problem 1) The Data-Each next-generation sequencing platform implements a different technology, but the workflow can be illustrated by a brief summary of the Illumina method 2  ...  National Institutes of Health under grant R01 HG006102 to SLS. Stefan Canzar received his Diploma in Computer  ... 
doi:10.1109/jproc.2015.2455551 pmid:28502990 pmcid:PMC5425171 fatcat:ic6d6z5ggbazdkaotcotdtbo3u

International Conference on Emerging Infectious Diseases 2018 Poster and Oral Presentation Abstracts

2018 Emerging Infectious Diseases  
The objective of this study is to evaluate MinION in detecting and sequencing of a variety of viral pathogens compared to Illumina MiSeq.  ...  plague, a fast and deadly form of pneumonia.  ...  The resistance plasmid repertoire was characterized using PacBio sequencing of >80 isolates with evidence of unique carbapenemase backgrounds, followed by mapping of all Illumina reads to the newly sequenced  ... 
doi:10.3201/eid2409.nn2409 fatcat:ba2ez7c45zg2plezo64wusdcqu