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PaSS: a sequencing simulator for PacBio sequencing

Wenmin Zhang, Ben Jia, Chaochun Wei
2019 BMC Bioinformatics  
Results: We developed a new PacBio Sequencing Simulator (PaSS). It can learn sequence patterns from PacBio sequencing data currently available.  ...  Assembly tests also suggest that reads simulated by PaSS are the most similar to experimental sequencing data. Conclusion: PaSS is an effective sequence simulator for PacBio sequencing.  ...  Acknowledgements We thank the High Performance Computing Center (HPCC) at Shanghai Jiao Tong University for the computation.  ... 
doi:10.1186/s12859-019-2901-7 fatcat:a46tpyjkena2hdf2vk4e5hyhly

NPBSS: a new PacBio sequencing simulator for generating the continuous long reads with an empirical model

Ze-Gang Wei, Shao-Wu Zhang
2018 BMC Bioinformatics  
Results: By analyzing the characteristic features of CLR data from PacBio SMRT (single molecule real time) sequencing, we developed a new PacBio sequencing simulator (called NPBSS) for producing CLR reads  ...  the quality value of raw PacBio datasets, especially for PacBio's continuous long reads (CLR).  ...  Acknowledgements We thank the editor as well as the reviewers for the valuable comments and suggestions, which have improved our paper.  ... 
doi:10.1186/s12859-018-2208-0 pmid:29788930 pmcid:PMC5964698 fatcat:mw4nwqcoyrb4dhsoqgle2lifue

2passtools: two-pass alignment using machine-learning-filtered splice junctions increases the accuracy of intron detection in long-read RNA sequencing

Matthew T Parker, Katarzyna Knop, Geoffrey J Barton, Gordon G Simpson
2021 Genome Biology  
two-pass approach.  ...  Here we apply alignment metrics and machine-learning-derived sequence information to filter spurious splice junctions from long-read alignments and use the remaining junctions to guide realignment in a  ...  Acknowledgements We thank James Abbott for testing the pipeline.  ... 
doi:10.1186/s13059-021-02296-0 pmid:33648554 pmcid:PMC7919322 fatcat:qpfsajynjndqjax5rzcikrbssi

Two-pass alignment using machine-learning-filtered splice junctions increases the accuracy of intron detection in long-read RNA sequencing [article]

Matthew T Parker, Geoffrey J Barton, Gordon G Simpson
2020 bioRxiv   pre-print
Here we present a two-pass approach, combining alignment metrics and machine-learning-derived sequence information to filter spurious examples from splice junctions identified in long-read alignments.  ...  Sequencing of full-length RNAs using long-reads reveals the true complexity of processing, however the relatively high error rates of long-read technologies can reduce the accuracy of intron identification  ...  Acknowledgments We thank James Abbott for testing the pipeline.  ... 
doi:10.1101/2020.05.27.118679 fatcat:xaoixbypbrhtpkgzscdpfpllsm

LongISLND:in silicosequencing of lengthy and noisy datatypes

Bayo Lau, Marghoob Mohiyuddin, John C. Mu, Li Tai Fang, Narges Bani Asadi, Carolina Dallett, Hugo Y. K. Lam
2016 Bioinformatics  
LongISLND is a software package designed to simulate sequencing data according to the characteristics of third generation, single-molecule sequencing technologies.  ...  The general software architecture is easily extendable, as demonstrated by the emulation of Pacific Biosciences (PacBio) multi-pass sequencing with P5 and P6 chemistries, producing data in FASTQ, H5, and  ...  Step N to N þ 5 of a series of extended-k-mer operations across a hypothetical truth sequence Number of flanking bases is taken to be a small value of 2 for illustration only.  ... 
doi:10.1093/bioinformatics/btw602 pmid:27667791 pmcid:PMC5167071 fatcat:ldeywo2bwzb6laiawm436fbc3i

PBSIM2: a simulator for long read sequencers with a novel generative model of quality scores

Yukiteru Ono, Kiyoshi Asai, Michiaki Hamada, Peter Robinson
2020 Bioinformatics  
Results To capture characteristics of errors in reads for long read sequencers, here, we introduce a generative model for quality scores, in which a hidden Markov Model with a latest model selection method  ...  Motivation Recent advances in high-throughput long-read sequencers, such as PacBio and Oxford Nanopore sequencers, produce longer reads with more errors than short-read sequencers.  ...  Martin Frith for his valuable comments on the manuscript. Computations in this study were partially performed on the supercomputer systems at the ROIS National Institute of Genetics.  ... 
doi:10.1093/bioinformatics/btaa835 pmid:32976553 pmcid:PMC8097687 fatcat:hml3m4w4cnej5ntb653ldple6y

Improved OTU-picking using long-read 16S rRNA gene amplicon sequencing and generic hierarchical clustering

Oscar Franzén, Jianzhong Hu, Xiuliang Bao, Steven H. Itzkowitz, Inga Peter, Ali Bashir
2015 Microbiome  
We implemented a complete-linkage hierarchical clustering strategy using a flexible computational pipeline, tailored specifically for PacBio circular consensus sequencing (CCS) data that outperforms heuristic  ...  Results: In simulated data, long-read sequencing was shown to improve OTU quality and decrease variance.  ...  We are thankful for the support from the genomics core facility for the library preparation and sequencing service and the computational resources provided by the Department of Scientific Computing at  ... 
doi:10.1186/s40168-015-0105-6 pmid:26434730 pmcid:PMC4593230 fatcat:3mj3doiaujbodbanb7qytktgou

SiLiCO: A Simulator of Long Read Sequencing in PacBio and Oxford Nanopore [article]

Ethan Alexander Garcia Baker, Sara Goodwin, W. Richard McCombie, Olivia Mendivil Ramos
2016 bioRxiv   pre-print
However, long read sequencing remains relatively expensive and error prone, and failed sequencing runs represent a significant problem for genomics core facilities.  ...  Here, we present SiLiCO, the first in silico simulation tool to generate standardized sequencing results from both of the leading long read sequenc-ing platforms.  ...  SiLiCO simulates both PacBio and, for the first time, Oxford Nanopore read sequencing results by stochastically generating genomic coordinates and extracting corresponding nucleotide sequences from a reference  ... 
doi:10.1101/076901 fatcat:p6jzcbpo35aa7moyjovgkavbpi

Testing the advantages and disadvantages of short- and long- read eukaryotic metagenomics using simulated reads

William S. Pearman, Nikki E. Freed, Olin K. Silander
2020 BMC Bioinformatics  
Here we compare simulated long reads from Oxford Nanopore and Pacific Biosciences (PacBio) with high accuracy Illumina read sets to systematically investigate the effects of sequence length and taxon type  ...  Because of the rapidly increasing popularity of this approach, a large number of computational tools and pipelines are available for analysing metagenomic data.  ...  Acknowledgements Thanks to Paul Gardner for his helpful and insightful comments on the manuscript. Thank you to two anonymous reviewers for their comments on the manuscript.  ... 
doi:10.1186/s12859-020-3528-4 pmid:32471343 fatcat:m6tr62bxs5chzeebfb27ofc344

Simulating The Dynamics Of Targeted Capture Sequencing With CapSim [article]

Minh Duc Cao, Devika Ganesamoorthy, Lachlan J. M. Coin
2017 bioRxiv   pre-print
Results: We developed CapSim, a software package for simulation of targeted sequencing.  ...  Given a genome sequence and a set of probes, CapSim simulates the fragmentation, the dynamics of probe hybridisation, and the sequencing of the captured fragments on Illumina and PacBio sequencing platforms  ...  Results Conclusion In this manuscript we have introduced CapSim a tool for simulation of targeted capture sequencing on both Illumina and PacBio platforms.  ... 
doi:10.1101/134510 fatcat:te4clsuabzh3pisfy76o6mb6xa

A benchmark of structural variation detection by long reads through a realistic simulated model

Nicolas Dierckxsens, Tong Li, Joris R. Vermeesch, Zhi Xie
2021 Genome Biology  
We develop Sim-it, a straightforward tool for the simulation of both structural variation and long-read data.  ...  AbstractAccurate simulations of structural variation distributions and sequencing data are crucial for the development and benchmarking of new tools.  ...  An additional filtering step was added for each output; we only retained variances that obtained a PASS for the FILTER value, that have a length of 50 bp or more and wherefore at least 3 (for sequencing  ... 
doi:10.1186/s13059-021-02551-4 pmid:34911553 pmcid:PMC8672642 fatcat:vf7zibujxrbbrikfwdrja6zmm4

A benchmark of structural variation detection by long reads through a realistic simulated model [article]

Nicolas Dierckxsens, Tong Li, Joris R. Vermeesch, Zhi Xie
2020 bioRxiv   pre-print
To achieve this, we developed Sim-it, a straightforward tool for the simulation of both structural variation and long-read data.  ...  These simulations from Sim-it revealed the strengths and weaknesses for current available structural variation callers and long read sequencing platforms.  ...  An additional filtering step was added for each VCF output; we only retained variances that obtained a PASS for the FILTER value, that have a length of 50 bp or more and wherefore at least 3 (for sequencing  ... 
doi:10.1101/2020.12.25.424397 fatcat:tm633vfubncffeqzsdqmivime4

TSD: A Computational Tool To Study the Complex Structural Variants Using PacBio Targeted Sequencing Data

Guofeng Meng, Ying Tan, Yue Fan, Yan Wang, Guang Yang, Gregory Fanning, Yang Qiu
2019 G3: Genes, Genomes, Genetics  
PacBio sequencing is a powerful approach to study DNA or RNA sequences in a longer scope.  ...  Here, we present a tool, TSD, for complex structural variant discovery using PacBio targeted sequencing data.  ...  Simulated PacBio reads We generated a set of simulated PacBio reads by randomly extracting the genomic DNA fragments and connecting them to form complex SVs.  ... 
doi:10.1534/g3.118.200900 pmid:30850377 pmcid:PMC6505135 fatcat:l6s6rjwhk5gnfinovjgqkzqwb4

Comparative analysis of targeted long read sequencing approaches for characterization of a plant's immune receptor repertoire

Michael Giolai, Pirita Paajanen, Walter Verweij, Kamil Witek, Jonathan D. G. Jones, Matthew D. Clark
2017 BMC Genomics  
The Oxford Nanopore Technologies MinION™ sequencer is a small, portable, low cost device that is accessible to labs of all sizes and attractive for in-the-field sequencing experiments.  ...  Here we demonstrate how MinION data can be used for RenSeq achieving similar results to the PacBio and how novel NLR gene fusions can be identified via a Nanopore RenSeq pipeline.  ...  Leggett and George Kettleborough for discussions about data evaluation and Darren Heavens for discussions about ONT MinION sequencing. We thank Ksenia K.  ... 
doi:10.1186/s12864-017-3936-7 pmid:28747151 pmcid:PMC5530509 fatcat:k4dqm2vvnzeddcjir4r3t4cq34

The effects of read length, quality and quantity on microsatellite discovery and primer development: from Illumina to PacBio

Na Wei, Jordan B. Bemmels, Christopher W. Dick
2014 Molecular Ecology Resources  
We outline a workflow from sequence quality control to microsatellite marker validation in three plant species using PacBio circular consensus sequencing (CCS).  ...  We then evaluate the performance of PacBio CCS in comparison with other NGS platforms for microsatellite isolation, through simulations that focus on variations in read length, read quantity and sequencing  ...  We thank the Smithsonian Tropical Research Institute and Center for Tropical Forest Science for facilitating fieldwork on Barro Colorado Island.  ... 
doi:10.1111/1755-0998.12245 pmid:24576200 fatcat:deuwzvzjfvfvbdlittzineklna
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