Genome sequence of the bacterioplanktonic, mixotrophic Vibrio campbellii strain PEL22A, isolated in the Abrolhos Bank.
J Bacteriol. 2012.
PMID: 22535939
Free PMC article.
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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.
In the relatively short time frame since 2005, the HT-NGS technologies are revolutionizing the human and animal genome researches by analysis of chromatin immunoprecipitation coupled to DNA microarray (ChIP-chip) or sequencing (ChIP-seq), RNA sequencing …
In the relatively short time frame since 2005, the HT-NGS technologies are revolutionizing the human and animal genome researches by …
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 …
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.
Whole genome sequencing provides the most comprehensive collection of an individual's genetic variation. ...We review methodologies for whole genome sequencing. There are two approaches for assembling short shotgun sequence reads into lon …
Whole genome sequencing provides the most comprehensive collection of an individual's genetic variation. ...We review m …
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 qualitie …
With fast development and wide applications of next-generation sequencing (NGS) technologies, genomic sequence informat …
The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.
Genome Res. 2010 Sep;20(9):1297-303. doi: 10.1101/gr.107524.110. Epub 2010 Jul 19.
Genome Res. 2010.
PMID: 20644199
Free PMC article.
Next-generation DNA sequencing (NGS) projects, such as the 1000 Genomes Project, are already revolutionizing our understanding of genetic variation among individuals. ...We conclude that the GATK programming framework enables developers and analysts to quickly and e …
Next-generation DNA sequencing (NGS) projects, such as the 1000 Genomes Project, are already revolutionizing our understanding …
Minimap2: pairwise alignment for nucleotide sequences.
Bioinformatics. 2018 Sep 15;34(18):3094-3100. doi: 10.1093/bioinformatics/bty191.
Bioinformatics. 2018.
PMID: 29750242
Free PMC article.
MOTIVATION: Recent advances in sequencing technologies promise ultra-long reads of 100 kb in average, full-length mRNA or cDNA reads in high throughput and genomic contigs over 100 Mb in length. ...RESULTS: Minimap2 is a general-purpose alignment program to map DNA …
MOTIVATION: Recent advances in sequencing technologies promise ultra-long reads of 100 kb in average, full-length mRNA or cDNA reads …
Analyzing Modern Biomolecules: The Revolution of Nucleic-Acid Sequencing - Review.
Biomolecules. 2021 Jul 28;11(8):1111. doi: 10.3390/biom11081111.
Biomolecules. 2021.
PMID: 34439777
Free PMC article.
Review.
The first allows to sequence small DNA fragments. The second one increases throughput, reducing turnaround and pricing, and is therefore more convenient to sequence full genomes and transcriptomes. ...Basic analyses and applications are now facilitated with n …
The first allows to sequence small DNA fragments. The second one increases throughput, reducing turnaround and pricing, and is theref …
Long-read sequencing of 111 rice genomes reveals significantly larger pan-genomes.
Genome Res. 2022 May;32(5):853-863. doi: 10.1101/gr.276015.121. Epub 2022 Apr 8.
Genome Res. 2022.
PMID: 35396275
Free PMC article.
The concept of pan-genome, which is the collection of all genomes from a population, has shown a great potential in genomics study, especially for crop sciences. ...Compared to NipRG, the long-read sequencing-based pan-genome constructed from 10 …
The concept of pan-genome, which is the collection of all genomes from a population, has shown a great potential in genomic …
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.
We present a method named HISAT2 (hierarchical indexing for spliced alignment of transcripts 2) that can align both DNA and RNA sequences using a graph Ferragina Manzini index. We use HISAT2 to represent and search an expanded model of the human reference genome in …
We present a method named HISAT2 (hierarchical indexing for spliced alignment of transcripts 2) that can align both DNA and RNA sequences …
PlasmidFinder and In Silico pMLST: Identification and Typing of Plasmid Replicons in Whole-Genome Sequencing (WGS).
Methods Mol Biol. 2020;2075:285-294. doi: 10.1007/978-1-4939-9877-7_20.
Methods Mol Biol. 2020.
PMID: 31584170
PlasmidFinder and in silico plasmid multiLocus sequence typing (pMLST) are two easy-to-use web tools for detection and characterization of plasmid sequences in whole-genome sequencing (WGS) data from Enterobacteriaceae. ...PlasmidFinder is usable for r …
PlasmidFinder and in silico plasmid multiLocus sequence typing (pMLST) are two easy-to-use web tools for detection and characterizati …
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