scholarly journals LoRTE: Detecting transposon-induced genomic variants using low coverage PacBio long read sequences

2016 ◽  
Author(s):  
Eric Disdero ◽  
Jonathan Filée
Keyword(s):  
Transposable Elements ◽  
Reference Genome ◽  
Genomic Analysis ◽  
Bioinformatic Tools ◽  
Sequencing Technologies ◽  
Population Genomic ◽  
Long Read ◽  
Different Strains ◽  
Low Coverage ◽  
Ncbi Blast

AbstractMotivationPopulation genomic analysis of transposable elements has greatly benefited from recent advances of sequencing technologies. However, the propensity of transposable elements to nest in highly repeated regions of genomes limits the efficiency of bioinformatic tools when short read sequences technology is used.ResultsLoRTE is the first tool able to use PacBio long read sequences to identify transposon deletions and insertions between a reference genome and genomes of different strains or populations. Tested against Drosophila melanogaster PacBio datasets, LoRTE appears to be a reliable and broadly applicable tools to study the dynamic and evolutionary impact of transposable elements using low coverage, long read sequences.Availability and ImplementationLoRTE is available at http://www.egce.cnrs-gif.fr/?p=6422. It is written in Python 2.7 and only requires the NCBI BLAST + package. LoRTE can be used on standard computer with limited RAM resources and reasonable running time even with large [email protected]

scholarly journals Illumina TruSeq synthetic long-reads empowerde novoassembly and resolve complex, highly repetitive transposable elements

2014 ◽  
Author(s):  
Rajiv C McCoy ◽  
Ryan W Taylor ◽  
Timothy A Blauwkamp ◽  
Joanna L Kelley ◽  
Michael Kertesz ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Reference Genome ◽  
De Novo ◽  
Model Organism ◽  
Genomic Analysis ◽  
High Sequence Identity ◽  
Current Reference ◽  
Sequencing Technologies ◽  
Long Reads ◽  
Whole Genomes

High-throughput DNA sequencing technologies have revolutionized genomic analysis, including thede novoassembly of whole genomes. Nevertheless, assembly of complex genomes remains challenging, in part due to the presence of dispersed repeats which introduce ambiguity during genome reconstruction. Transposable elements (TEs) can be particularly problematic, especially for TE families exhibiting high sequence identity, high copy number, or present in complex genomic arrangements. While TEs strongly affect genome function and evolution, most currentde novoassembly approaches cannot resolve long, identical, and abundant families of TEs. Here, we applied a novel Illumina technology called TruSeq synthetic long-reads, which are generated through highly parallel library preparation and local assembly of short read data and achieve lengths of 1.5-18.5 Kbp with an extremely low error rate (∼0.03% per base). To test the utility of this technology, we sequenced and assembled the genome of the model organismDrosophila melanogaster(reference genome strainy;cn,bw,sp) achieving an N50 contig size of 69.7 Kbp and covering 96.9% of the euchromatic chromosome arms of the current reference genome. TruSeq synthetic long-read technology enables placement of individual TE copies in their proper genomic locations as well as accurate reconstruction of TE sequences. We entirely recovered and accurately placed 4,229 (77.8%) of the 5,434 of annotated transposable elements with perfect identity to the current reference genome. As TEs are ubiquitous features of genomes of many species, TruSeq synthetic long- reads, and likely other methods that generate long reads, offer a powerful approach to improvede novoassemblies of whole genomes.

scholarly journals Complete Genome Resequencing of Thermus thermophilus Strain TMY by Hybrid Assembly of Long- and Short-Read Sequencing Technologies

2021 ◽  
Vol 10 (46) ◽  
Author(s):  
Kentaro Miyazaki ◽  
Natsuko Tokito
Keyword(s):  
Complete Genome ◽  
Thermus Thermophilus ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Hybrid Assembly ◽  
Genome Resequencing ◽  
Short Read ◽  
Content Type ◽  
Sequencing Technologies ◽  
Long Read

Complete genome resequencing was conducted for Thermus thermophilus strain TMY by hybrid assembly of Oxford Nanopore Technologies long-read and MGI short-read data. Errors in the previously reported genome sequence determined by PacBio technology alone were corrected, allowing for high-quality comparative genomic analysis of closely related T. thermophilus genomes.

scholarly journals Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies

BMC Biology ◽  
2020 ◽  
Vol 18 (1) ◽  
Author(s):  
Robert M. Waterhouse ◽  
Sergey Aganezov ◽  
Yoann Anselmetti ◽  
Jiyoung Lee ◽  
Livio Ruzzante ◽  
...  
Keyword(s):  
Anopheles Funestus ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Financial Barriers ◽  
Complementary Method ◽  
Gene Synteny ◽  
Sequencing Technologies ◽  
Complementary Approach ◽  
Long Read ◽  
Gene Order Conservation

Abstract Background New sequencing technologies have lowered financial barriers to whole genome sequencing, but resulting assemblies are often fragmented and far from ‘finished’. Updating multi-scaffold drafts to chromosome-level status can be achieved through experimental mapping or re-sequencing efforts. Avoiding the costs associated with such approaches, comparative genomic analysis of gene order conservation (synteny) to predict scaffold neighbours (adjacencies) offers a potentially useful complementary method for improving draft assemblies. Results We evaluated and employed 3 gene synteny-based methods applied to 21 Anopheles mosquito assemblies to produce consensus sets of scaffold adjacencies. For subsets of the assemblies, we integrated these with additional supporting data to confirm and complement the synteny-based adjacencies: 6 with physical mapping data that anchor scaffolds to chromosome locations, 13 with paired-end RNA sequencing (RNAseq) data, and 3 with new assemblies based on re-scaffolding or long-read data. Our combined analyses produced 20 new superscaffolded assemblies with improved contiguities: 7 for which assignments of non-anchored scaffolds to chromosome arms span more than 75% of the assemblies, and a further 7 with chromosome anchoring including an 88% anchored Anopheles arabiensis assembly and, respectively, 73% and 84% anchored assemblies with comprehensively updated cytogenetic photomaps for Anopheles funestus and Anopheles stephensi. Conclusions Experimental data from probe mapping, RNAseq, or long-read technologies, where available, all contribute to successful upgrading of draft assemblies. Our evaluations show that gene synteny-based computational methods represent a valuable alternative or complementary approach. Our improved Anopheles reference assemblies highlight the utility of applying comparative genomics approaches to improve community genomic resources.

scholarly journals Rapid Low-Cost Assembly of the Drosophila melanogaster Reference Genome Using Low-Coverage, Long-Read Sequencing

2018 ◽  
Vol 8 (10) ◽  
pp. 3143-3154 ◽  
Author(s):  
Edwin A. Solares ◽  
Mahul Chakraborty ◽  
Danny E. Miller ◽  
Shannon Kalsow ◽  
Kate Hall ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Reference Genome ◽  
Low Cost ◽  
Long Read ◽  
Low Coverage

scholarly journals QAlign: Aligning nanopore reads accurately using current-level modeling

2019 ◽  
Author(s):  
Dhaivat Joshi ◽  
Shunfu Mao ◽  
Sreeram Kannan ◽  
Suhas Diggavi
Keyword(s):  
Reference Genome ◽  
Genomic Analysis ◽  
Vital Role ◽  
High Error Rate ◽  
Sequencing Technology ◽  
Long Reads ◽  
A Genome ◽  
Long Read ◽  
Nanopore Sequencer ◽  
Sequencing Process

AbstractMotivationEfficient and accurate alignment of DNA / RNA sequence reads to each other or to a reference genome / transcriptome is an important problem in genomic analysis. Nanopore sequencing has emerged as a major sequencing technology and many long-read aligners have been designed for aligning nanopore reads. However, the high error rate makes accurate and efficient alignment difficult. Utilizing the noise and error characteristics inherent in the sequencing process properly can play a vital role in constructing a robust aligner. In this paper, we design QAlign, a pre-processor that can be used with any long-read aligner for aligning long reads to a genome / transcriptome or to other long reads. The key idea in QAlign is to convert the nucleotide reads into discretized current levels that capture the error modes of the nanopore sequencer before running it through a sequence aligner.ResultsWe show that QAlign is able to improve alignment rates from around 80% up to 90% with nanopore reads when aligning to the genome. We also show that QAlign improves the average overlap quality by 9.2%, 2.5% and 10.8% in three real datasets for read-to-read alignment. Read-to-transcriptome alignment rates are improved from 51.6% to 75.4% and 82.6% to 90% in two real datasets.Availabilityhttps://github.com/joshidhaivat/QAlign.git

scholarly journals Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies

2018 ◽  
Author(s):  
Robert M. Waterhouse ◽  
Sergey Aganezov ◽  
Yoann Anselmetti ◽  
Jiyoung Lee ◽  
Livio Ruzzante ◽  
...  
Keyword(s):  
Anopheles Funestus ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Financial Barriers ◽  
Complementary Method ◽  
Gene Synteny ◽  
Sequencing Technologies ◽  
Complementary Approach ◽  
Long Read ◽  
Gene Order Conservation

AbstractBackgroundNew sequencing technologies have lowered financial barriers to whole genome sequencing, but resulting assemblies are often fragmented and far from ‘finished’. Updating multi-scaffold drafts to chromosome-level status can be achieved through experimental mapping or re-sequencing efforts. Avoiding the costs associated with such approaches, comparative genomic analysis of gene order conservation (synteny) to predict scaffold neighbours (adjacencies) offers a potentially useful complementary method for improving draft assemblies.ResultsWe employed three gene synteny-based methods applied to 21 Anopheles mosquito assemblies to produce consensus sets of scaffold adjacencies. For subsets of the assemblies we integrated these with additional supporting data to confirm and complement the synteny-based adjacencies: six with physical mapping data that anchor scaffolds to chromosome locations, 13 with paired-end RNA sequencing (RNAseq) data, and three with new assemblies based on re-scaffolding or Pacific Biosciences long-read data. Our combined analyses produced 20 new superscaffolded assemblies with improved contiguities: seven for which assignments of non-anchored scaffolds to chromosome arms span more than 75% of the assemblies, and a further seven with chromosome anchoring including an 88% anchored Anopheles arabiensis assembly and, respectively, 73% and 84% anchored assemblies with comprehensively updated cytogenetic photomaps for Anopheles funestus and Anopheles stephensi.ConclusionsExperimental data from probe mapping, RNAseq, or long-read technologies, where available, all contribute to successful upgrading of draft assemblies. Our comparisons show that gene synteny-based computational methods represent a valuable alternative or complementary approach. Our improved Anopheles reference assemblies highlight the utility of applying comparative genomics approaches to improve community genomic resources.

scholarly journals Construction of a chromosome-scale long-read reference genome assembly for potato

GigaScience ◽  
2020 ◽  
Vol 9 (9) ◽  
Author(s):  
Gina M Pham ◽  
John P Hamilton ◽  
Joshua C Wood ◽  
Joseph T Burke ◽  
Hainan Zhao ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Reference Genome ◽  
Agronomic Traits ◽  
Solanum Tuberosum L ◽  
Fold Increase ◽  
High Quality ◽  
Sequencing Technologies ◽  
Oxford Nanopore ◽  
Long Read ◽  
Oxford Nanopore Technologies

Abstract Background Worldwide, the cultivated potato, Solanum tuberosum L., is the No. 1 vegetable crop and a critical food security crop. The genome sequence of DM1–3 516 R44, a doubled monoploid clone of S. tuberosum Group Phureja, was published in 2011 using a whole-genome shotgun sequencing approach with short-read sequence data. Current advanced sequencing technologies now permit generation of near-complete, high-quality chromosome-scale genome assemblies at minimal cost. Findings Here, we present an updated version of the DM1–3 516 R44 genome sequence (v6.1) using Oxford Nanopore Technologies long reads coupled with proximity-by-ligation scaffolding (Hi-C), yielding a chromosome-scale assembly. The new (v6.1) assembly represents 741.6 Mb of sequence (87.8%) of the estimated 844 Mb genome, of which 741.5 Mb is non-gapped with 731.2 Mb anchored to the 12 chromosomes. Use of Oxford Nanopore Technologies full-length complementary DNA sequencing enabled annotation of 32,917 high-confidence protein-coding genes encoding 44,851 gene models that had a significantly improved representation of conserved orthologs compared with the previous annotation. The new assembly has improved contiguity with a 595-fold increase in N50 contig size, 99% reduction in the number of contigs, a 44-fold increase in N50 scaffold size, and an LTR Assembly Index score of 13.56, placing it in the category of reference genome quality. The improved assembly also permitted annotation of the centromeres via alignment to sequencing reads derived from CENH3 nucleosomes. Conclusions Access to advanced sequencing technologies and improved software permitted generation of a high-quality, long-read, chromosome-scale assembly and improved annotation dataset for the reference genotype of potato that will facilitate research aimed at improving agronomic traits and understanding genome evolution.

scholarly journals Construction of a new chromosome-scale, long-read reference genome assembly of the Syrian hamster, Mesocricetus auratus

2021 ◽  
Author(s):  
R. Alan Harris ◽  
Muthuswamy Raveendran ◽  
Dustin T Lyfoung ◽  
Fritz J Sedlazeck ◽  
Medhat Mahmoud ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Syrian Hamster ◽  
Reference Genome ◽  
Sequence Data ◽  
Mesocricetus Auratus ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Sequencing Technologies ◽  
Long Read ◽  
Short Read Sequence

Background The Syrian hamster (Mesocricetus auratus) has been suggested as a useful mammalian model for a variety of diseases and infections, including infection with respiratory viruses such as SARS-CoV-2. The MesAur1.0 genome assembly was published in 2013 using whole-genome shotgun sequencing with short-read sequence data. Current more advanced sequencing technologies and assembly methods now permit the generation of near-complete genome assemblies with higher quality and higher continuity. Findings Here, we report an improved assembly of the M. auratus genome (BCM_Maur_2.0) using Oxford Nanopore Technologies long-read sequencing to produce a chromosome-scale assembly. The total length of the new assembly is 2.46 Gbp, similar to the 2.50 Gbp length of a previous assembly of this genome, MesAur1.0. BCM_Maur_2.0 exhibits significantly improved continuity with a scaffold N50 that is 6.7 times greater than MesAur1.0. Furthermore, 21,616 protein coding genes and 10,459 noncoding genes were annotated in BCM_Maur_2.0 compared to 20,495 protein coding genes and 4,168 noncoding genes in MesAur1.0. This new assembly also improves the unresolved regions as measured by nucleotide ambiguities, where approximately 17.11% of bases in MesAur1.0 were unresolved compared to BCM_Maur_2.0 in which the number of unresolved bases is reduced to 3.00%. Conclusions Access to a more complete reference genome with improved accuracy and continuity will facilitate more detailed, comprehensive, and meaningful research results for a wide variety of future studies using Syrian hamsters as models.

scholarly journals HISAT-genotype: Next Generation Genomic Analysis Platform on a Personal Computer

2018 ◽  
Author(s):  
Daehwan Kim ◽  
Joseph Paggi ◽  
Steven L. Salzberg
Keyword(s):  
Reference Genome ◽  
Search Algorithm ◽  
Genomic Analysis ◽  
Hla Typing ◽  
Next Generation ◽  
Desktop Computer ◽  
Human Organ ◽  
Human Reference Genome ◽  
Sequencing Technologies ◽  
Analysis Platform

AbstractRapid advances in next-generation sequencing technologies have dramatically changed our ability to perform genome-scale analyses of human genomes. The human reference genome used for most genomic analyses represents only a small number of individuals, limiting its usefulness for genotyping. We designed a novel method, HISAT-genotype, for representing and searching an expanded model of the human reference genome, in which a comprehensive catalogue of known genomic variants and haplotypes is incorporated into the data structure used for searching and alignment. This strategy for representing a population of genomes, along with a very fast and memory-efficient search algorithm, enables more detailed and accurate variant analyses than previous methods. We demonstrate HISAT-genotype’s accuracy for HLA typing, a critical task in human organ transplantation, and for the DNA fingerprinting tests widely used in forensics. In both applications, HISAT-genotype not only improves upon earlier computational methods, but matches or exceeds the accuracy of laboratory-based assays.One Sentence SummaryHISAT-genotype is a software platform that has the ability to genotype all the genes in an individual’s genome within a few hours on a desktop computer.

scholarly journals Tools and best practices for retrotransposon analysis using high-throughput sequencing data

Mobile DNA ◽  
2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Aurélie Teissandier ◽  
Nicolas Servant ◽  
Emmanuel Barillot ◽  
Deborah Bourc’his
Keyword(s):  
Transposable Elements ◽  
Transposable Element ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
Reference Genome ◽  
Repetitive Sequences ◽  
Simulated Data ◽  
Sequencing Data ◽  
Sequencing Technologies ◽  
Human Genomes

Abstract Background Sequencing technologies give access to a precise picture of the molecular mechanisms acting upon genome regulation. One of the biggest technical challenges with sequencing data is to map millions of reads to a reference genome. This problem is exacerbated when dealing with repetitive sequences such as transposable elements that occupy half of the mammalian genome mass. Sequenced reads coming from these regions introduce ambiguities in the mapping step. Therefore, applying dedicated parameters and algorithms has to be taken into consideration when transposable elements regulation is investigated with sequencing datasets. Results Here, we used simulated reads on the mouse and human genomes to define the best parameters for aligning transposable element-derived reads on a reference genome. The efficiency of the most commonly used aligners was compared and we further evaluated how transposable element representation should be estimated using available methods. The mappability of the different transposon families in the mouse and the human genomes was calculated giving an overview into their evolution. Conclusions Based on simulated data, we provided recommendations on the alignment and the quantification steps to be performed when transposon expression or regulation is studied, and identified the limits in detecting specific young transposon families of the mouse and human genomes. These principles may help the community to adopt standard procedures and raise awareness of the difficulties encountered in the study of transposable elements.

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