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ABACAS: algorithm-based automatic contiguation of assembled sequences

S. Assefa, T. M. Keane, T. D. Otto, C. Newbold, M. Berriman
2009 Bioinformatics  
Recently a number of de novo and mapping based assemblers have been developed to produce high quality draft genomes from second generation sequencing technology reads.  ...  However, a significant amount of manual effort is still required to go from the point of having a draft assembly to obtaining a fully contiguated genome.  ... 
doi:10.1093/bioinformatics/btp347 pmid:19497936 pmcid:PMC2712343 fatcat:q3bqwp77zfburlp6sxed32uap4

CONTIGuator: a bacterial genomes finishing tool for structural insights on draft genomes

Marco Galardini, Emanuele G Biondi, Marco Bazzicalupo, Alessio Mengoni
2011 Source Code for Biology and Medicine  
However, a limiting step of genome sequencing is the finishing process, needed to infer the relative position of each contig and close sequencing gaps.  ...  Here we present CONTIGuator, a software tool for contigs mapping over a reference genome which allows the visualization of a map of contigs, underlining loss and/or gain of genetic elements and permitting  ...  and Samuel Assefa for the feedbacks on ABACAS.  ... 
doi:10.1186/1751-0473-6-11 pmid:21693004 pmcid:PMC3133546 fatcat:zkrtllxqgncnff5gbuvmqhtigy

A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs

Martin T Swain, Isheng J Tsai, Samual A Assefa, Chris Newbold, Matthew Berriman, Thomas D Otto
2012 Nature Protocols  
Genome projects now produce draft assemblies within weeks thanks to advanced high-throughput sequencing technologies.  ...  It offers flexible functionality to close gaps in scaffolds, correct base errors in the consensus sequence, and to exploit reference genomes (if available) for improving scaffolding and generating annotations  ...  ABACAS: Algorithm Based Automatic Contiguation of Assembled Sequences ABACAS 13 is designed to help with sequencing closely-related strains, where a high quality reference sequence is available.  ... 
doi:10.1038/nprot.2012.068 pmid:22678431 pmcid:PMC3648784 fatcat:g4q77e4nvnfvfpr4lnprpsxhaq

CAR: contig assembly of prokaryotic draft genomes using rearrangements

Chin Lung Lu, Kun-Tze Chen, Shih-Yuan Huang, Hsien-Tai Chiu
2014 BMC Bioinformatics  
Next generation sequencing technology has allowed efficient production of draft genomes for many organisms of interest.  ...  For validation, we have tested CAR on a real dataset composed of several prokaryotic genomes and also compared its performance with several other reference-based contig assembly tools.  ...  Acknowledgements This work was supported in part by National Science Council of Taiwan under grant NSC100-2221-E-007-129-MY3. Received: 11 July 2014 Accepted: 5 November 2014  ... 
doi:10.1186/s12859-014-0381-3 pmid:25431302 pmcid:PMC4253983 fatcat:2ffjk3x26nhvnhii6ask4mayd4

Emergence of Vancomycin-Resistant Enterococcus faecium at an Australian Hospital: A Whole Genome Sequencing Analysis

Kelvin W. C. Leong, Louise A. Cooley, Tara L. Anderson, Sanjay S. Gautam, Belinda McEwan, Anne Wells, Fiona Wilson, Lucy Hughson, Ronan F. O'Toole
2018 Scientific Reports  
We report here the draft whole-genome sequence of a newly designated VREfm sequence type, sequence type 1421 (ST1421).  ...  The spread of vancomycin-resistant Enterococcus faecium (VREfm) has become a challenge to health care infection control worldwide.  ...  ACKNOWLEDGMENT We gratefully acknowledge the support of the Royal Hobart Hospital Research Foundation.  ... 
doi:10.1038/s41598-018-24614-6 pmid:29674657 pmcid:PMC5908837 fatcat:4qvwy2pzr5dazedcgchaz6awqq

Draft Genome Sequence of New Vancomycin-Resistant Enterococcus faecium Sequence Type 1421

Kelvin W. C. Leong, Louise A. Cooley, Ronan F. O'Toole
2018 Genome Announcements  
We report here the draft whole-genome sequence of a newly designated VREfm sequence type, sequence type 1421 (ST1421).  ...  The spread of vancomycin-resistant Enterococcus faecium (VREfm) has become a challenge to health care infection control worldwide.  ...  ACKNOWLEDGMENT We gratefully acknowledge the support of the Royal Hobart Hospital Research Foundation.  ... 
doi:10.1128/genomea.00438-18 pmid:29773638 pmcid:PMC5958267 fatcat:duj7olej4ffp5ifycfve2haeyu

Chloroplast genome assembly approaches from NGS data

Zdravka Ivanova, Evelina Daskalova, Georgi Minkov, Vesselin Baev
2016 Journal of BioScience and Biotechnology  
The advent of Next Generation Sequencing platforms led to increase of research in whole genome assembly algorithms and software.  ...  In response to this, several new assemblers were developed specifically for de novo assembly of next generation sequencing.  ...  Abacas ABACAS (Algorithm Based Automatic Contiguation of Assembled Sequences) is developed for aligning, ordering and orientating assembled contigs based on a reference genome (Assefa et al. 2009 ).  ... 
doaj:eac31aba8fd34b59bd9e96c6893d7111 fatcat:f4tvhbwvdnakxosra2reudwmzq

Approaches for in silico finishing of microbial genome sequences

Frederico Schmitt Kremer, Alan John Alexander McBride, Luciano da Silva Pinto
2017 Genetics and Molecular Biology  
The introduction of next-generation sequencing (NGS) had a significant effect on the availability of genomic information, leading to an increase in the number of sequenced genomes from a large spectrum  ...  Unfortunately, due to the limitations implied by the short-read sequencing platforms, most of these newly sequenced genomes remained as "drafts", incomplete representations of the whole genetic content  ...  ABACAS (Algorithm-based Automatic Contiguation of Assembled Sequences) (Assefa et al., 2009 ): can use NUCmer or PROmer from the MUMmer (Kurtz et al., 2004) package to align the contigs against a reference  ... 
doi:10.1590/1678-4685-gmb-2016-0230 pmid:28898352 pmcid:PMC5596377 fatcat:u37yjmj5pjcgfms2rfaghqkxve

First report of reference guided genome assembly of Black Bengal goat (Capra hircus) [article]

AMAM Zonaed Siddiki, Abdul Baten, Masum Billah, Mohammad Atique Ul Alam, Kazi Shefaul Mulk Shawrob, Sourav Saha, Muntaha Chowdhury, Atif Hasan Rahman, Michael Stear, Gous Miah, Mahadia Kumkum, Mohammad Alamgir Hossain (+2 others)
2019 bioRxiv   pre-print
The genomic DNA of local (Chittagong, Bangladesh) healthy Black Bengal goat (Capra hircus) was extracted and then sequenced. The de novo assembly and structural annotations are being presented here.  ...  Universal Single Copy Orthologs refer 82.5% completeness of the assembled genome.  ...  Acknowledgments Authors concede the support of Beijing Genomic Institute for the sequencing service and that of Southern Cross University, Lismore, Australia for the computational support.  ... 
doi:10.1101/603266 fatcat:eigoi4z4cbbfplybg7yifav34u

The genome of the Black Bengal goat (Capra hircus)

Amam Zonaed Siddiki, Abdul Baten, Masum Billah, Mohammad Atique Ul Alam, Kazi Shefaul Mulk Shawrob, Sourav Saha, Muntaha Chowdhury, Atif Hasan Rahman, Michael Stear, Gous Miah, Mahadia Kumkum, Mohammad Sirazul Islam (+3 others)
2019 BMC Research Notes  
Sequencing was completed using the Illumina HiSeq 2500 sequencing platform and the draft assembly was generated using the "ARS1" genome as the reference.  ...  Genome completeness was assessed using BUSCO (Benchmarking Universal Single-Copy Orthologs) which showed 82.5% completeness of the assembled genome.  ...  orthologs; ABACAS: algorithm-based automatic contiguation of assembled sequences; Gb: giga base pair; Mb: megabase pair; Kb: kilobase pair; bp: base pair; GO: gene ontology; gDNA: genomic DNA; PCR: polymerase  ... 
doi:10.1186/s13104-019-4400-3 pmid:31248431 pmcid:PMC6598337 fatcat:e7c7qxe4g5d55ph4x7runuabmy

The hidden perils of read mapping as a quality assessment tool in genome sequencing

B. Lehri, A. M. Seddon, A. V. Karlyshev
2017 Scientific Reports  
This article provides a comparative analysis of the various methods of genome sequencing focusing on verification of the assembly quality.  ...  The results of a comparative assessment of various de novo assembly tools, as well as sequencing technologies, are presented using a recently completed sequence of the genome of Lactobacillus fermentum  ...  Acknowledgements Special thanks to Aaron Caffrey for helping out with running some of the software Author Contributions B.L. and A.V.K., conceived the study, performed the experiments, wrote the manuscript  ... 
doi:10.1038/srep43149 pmid:28225089 pmcid:PMC5320493 fatcat:egqut6ue5rh73iyv3fi3vxqthi

Challenges, Solutions, and Quality Metrics of Personal Genome Assembly in Advancing Precision Medicine

Wenming Xiao, Leihong Wu, Gokhan Yavas, Vahan Simonyan, Baitang Ning, Huixiao Hong
2016 Pharmaceutics  
In this review, we introduce the history of human genome sequencing and the evolution of sequencing platforms, from Sanger sequencing to emerging "third generation sequencing" technologies.  ...  Even though each of us shares more than 99% of the DNA sequences in our genome, there are millions of sequence codes or structure in small regions that differ between individuals, giving us different characteristics  ...  Acknowledgments: Leihong Wu is grateful to the National Center for Toxicological Research (NCTR) of the  ... 
doi:10.3390/pharmaceutics8020015 pmid:27110816 pmcid:PMC4932478 fatcat:xkrhpx36s5ffxjejq2unw67ccm

WiseScaffolder: an algorithm for the semi-automatic scaffolding of Next Generation Sequencing data

Gregory K. Farrant, Mark Hoebeke, Frédéric Partensky, Gwendoline Andres, Erwan Corre, Laurence Garczarek
2015 BMC Bioinformatics  
The sequencing depth provided by high-throughput sequencing technologies has allowed a rise in the number of de novo sequenced genomes that could potentially be closed without further sequencing.  ...  For all three model organisms, WiseScaffolder produced better results than other scaffolders in terms of contiguity statistics (number of genome fragments, N50, LG50, etc.) and, in the case of WH8103,  ...  We thank the Genoscope, particularly Karine Labadie, Jean-Marc Aury and Patrick Wincker, for whole genome sequencing of Synechococcus sp.  ... 
doi:10.1186/s12859-015-0705-y pmid:26335184 pmcid:PMC4559175 fatcat:s5bby5ew45dcxcf6zmtn2yyjbi

From Sequence Mapping to Genome Assemblies [chapter]

Thomas D. Otto
2014 Msphere  
The development of "next-generation" high-throughput sequencing technologies has made it possible for many labs to undertake sequencing-based research projects that were unthinkable just a few years ago  ...  In this chapter, we fi rst discuss some limitations of the mapping process and how these may be overcome through local sequence assembly.  ...  Introduction The aim of sequence assembly is to join short sequences of n ucleotides (sequence reads 35-1,000 bp in length) into contiguous sequences (contigs) that represent the sequenced DNA.  ... 
doi:10.1007/978-1-4939-1438-8_2 pmid:25388106 fatcat:dobmztvzlbctbf6yjz24cshake

Modern technologies and algorithms for scaffolding assembled genomes

Jay Ghurye, Mihai Pop, Nicola Segata
2019 PLoS Computational Biology  
Here, we survey these technologies and the algorithms used to assemble and analyze large eukaryotic genomes, placed within the historical context of genome scaffolding technologies that have been in existence  ...  Recent technologies originally designed to capture chromatin structure have been shown to effectively complement sequencing data, leading to much more contiguous reconstructions of genomes than previously  ...  In vitro, long-range sequence information for de novo genome assembly via transposase contiguity.  ... 
doi:10.1371/journal.pcbi.1006994 pmid:31166948 pmcid:PMC6550390 fatcat:3cxdpvhs2faifj35iciodxnbt4
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