Genome sequence of the human pathogen Vibrio cholerae Amazonia.
J Bacteriol. 2011.
PMID: 21952545
Free PMC article.
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genome sequence or the human pathogen vibrio cholerae amazonia
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Genome sequence of the human pathogen Vibrio cholerae Amazonia
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The Sequence Alignment/Map format and SAMtools.
Bioinformatics. 2009 Aug 15;25(16):2078-9. doi: 10.1093/bioinformatics/btp352. Epub 2009 Jun 8.
Bioinformatics. 2009.
PMID: 19505943
Free PMC article.
SUMMARY: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compac …
SUMMARY: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference seque …
What is next generation sequencing?
Arch Dis Child Educ Pract Ed. 2013 Dec;98(6):236-8. doi: 10.1136/archdischild-2013-304340. Epub 2013 Aug 28.
Arch Dis Child Educ Pract Ed. 2013.
PMID: 23986538
Free PMC article.
Review.
Next generation sequencing (NGS), massively parallel or deep sequencing are related terms that describe a DNA sequencing technology which has revolutionised genomic research. Using NGS an entire human genome can be sequenced within …
Next generation sequencing (NGS), massively parallel or deep sequencing are related terms that describe a DNA sequencing …
Sequencing technologies and genome sequencing.
J Appl Genet. 2011 Nov;52(4):413-35. doi: 10.1007/s13353-011-0057-x. Epub 2011 Jun 23.
J Appl Genet. 2011.
PMID: 21698376
Free PMC article.
Review.
The high-throughput - next generation sequencing (HT-NGS) technologies are currently the hottest topic in the field of human and animals genomics researches, which can produce over 100 times more data compared to the most sophisticated capillary sequencers …
The high-throughput - next generation sequencing (HT-NGS) technologies are currently the hottest topic in the field of human a …
Whole genome sequencing.
Methods Mol Biol. 2010;628:215-26. doi: 10.1007/978-1-60327-367-1_12.
Methods Mol Biol. 2010.
PMID: 20238084
Review.
We review methodologies for whole genome sequencing. There are two approaches for assembling short shotgun sequence reads into longer contiguous genomic sequences. ...We expect methodologies to evolve rapidly as sequencing technologies im …
We review methodologies for whole genome sequencing. There are two approaches for assembling short shotgun sequence rea …
Comparison of next-generation sequencing systems.
J Biomed Biotechnol. 2012;2012:251364. doi: 10.1155/2012/251364. Epub 2012 Jul 5.
J Biomed Biotechnol. 2012.
PMID: 22829749
Free PMC article.
Review.
With fast development and wide applications of next-generation sequencing (NGS) technologies, genomic sequence information is within reach to aid the achievement of goals to decode life mysteries, make better crops, detect pathogens, and improve life q …
With fast development and wide applications of next-generation sequencing (NGS) technologies, genomic sequence informat …
Fast and accurate long-read alignment with Burrows-Wheeler transform.
Bioinformatics. 2010 Mar 1;26(5):589-95. doi: 10.1093/bioinformatics/btp698. Epub 2010 Jan 15.
Bioinformatics. 2010.
PMID: 20080505
Free PMC article.
MOTIVATION: Many programs for aligning short sequencing reads to a reference genome have been developed in the last 2 years. ...RESULTS: We designed and implemented a new algorithm, Burrows-Wheeler Aligner's Smith-Waterman Alignment (BWA-SW), to align long …
MOTIVATION: Many programs for aligning short sequencing reads to a reference genome have been developed in the last 2 years. . …
Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype.
Nat Biotechnol. 2019 Aug;37(8):907-915. doi: 10.1038/s41587-019-0201-4. Epub 2019 Aug 2.
Nat Biotechnol. 2019.
PMID: 31375807
Free PMC article.
The human reference genome represents only a small number of individuals, which limits its usefulness for genotyping. We present a method named HISAT2 (hierarchical indexing for spliced alignment of transcripts 2) that can align both DNA and RNA sequences usi …
The human reference genome represents only a small number of individuals, which limits its usefulness for genotyping. We prese …
New Approaches for Genome Assembly and Scaffolding.
Annu Rev Anim Biosci. 2019 Feb 15;7:17-40. doi: 10.1146/annurev-animal-020518-115344. Epub 2018 Nov 28.
Annu Rev Anim Biosci. 2019.
PMID: 30485757
Review.
Affordable, high-throughput DNA sequencing has accelerated the pace of genome assembly over the past decade. Genome assemblies from high-throughput, short-read sequencing, however, are often not as contiguous as the first generation of genome as …
Affordable, high-throughput DNA sequencing has accelerated the pace of genome assembly over the past decade. Genome ass …
Insights from 20 years of bacterial genome sequencing.
Funct Integr Genomics. 2015 Mar;15(2):141-61. doi: 10.1007/s10142-015-0433-4. Epub 2015 Feb 27.
Funct Integr Genomics. 2015.
PMID: 25722247
Free PMC article.
Review.
Using third-generation DNA sequencing, it is possible to completely sequence a bacterial genome in a few hours and identify some types of methylation sites along the genome as well. Sequencing of bacterial genome sequences is now a …
Using third-generation DNA sequencing, it is possible to completely sequence a bacterial genome in a few hours and iden …
Human Genome Sequencing at the Population Scale: A Primer on High-Throughput DNA Sequencing and Analysis.
Am J Epidemiol. 2017 Oct 15;186(8):1000-1009. doi: 10.1093/aje/kww224.
Am J Epidemiol. 2017.
PMID: 29040395
Free PMC article.
Review.
Massively parallel high-throughput sequencing technology, where DNA is sheared into smaller pieces, sequenced, and then computationally reordered and analyzed, enables fast and affordable sequencing of full human genomes. As the price of sequ …
Massively parallel high-throughput sequencing technology, where DNA is sheared into smaller pieces, sequenced, and then comput …