An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations DOI Creative Commons
Bernardo Clavijo, Luca Venturini, Christian Schudoma

et al.

Genome Research, Journal Year: 2017, Volume and Issue: 27(5), P. 885 - 896

Published: April 18, 2017

Advances in genome sequencing and assembly technologies are generating many high-quality sequences, but assemblies of large, repeat-rich polyploid genomes, such as that bread wheat, remain fragmented incomplete. We have generated a new wheat whole-genome shotgun sequence using combination optimized data types an algorithm designed to deal with large complex genomes. The represents >78% the scaffold N50 88.8 kb has high fidelity input data. Our annotation combines strand-specific Illumina RNA-seq Pacific Biosciences (PacBio) full-length cDNAs identify 104,091 high-confidence protein-coding genes 10,156 noncoding RNA genes. confirmed three known identified one novel rearrangements. approach enables rapid scalable identification structural variants, definition complete gene models, all powerful resources for trait analysis breeding this key global crop.

Language: Английский

The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes DOI Creative Commons
Todd J. Treangen, Brian Ondov, Sergey Koren

et al.

Genome biology, Journal Year: 2014, Volume and Issue: 15(11)

Published: Nov. 19, 2014

Abstract Whole-genome sequences are now available for many microbial species and clades, however existing whole-genome alignment methods limited in their ability to perform sequence comparisons of multiple simultaneously. Here we present the Harvest suite core-genome visualization tools rapid simultaneous analysis thousands intraspecific strains. includes Parsnp, a fast multi-aligner, Gingr, dynamic visual platform. Together they provide interactive alignments, variant calls, recombination detection, phylogenetic trees. Using simulated real data demonstrate that our approach exhibits unrivaled speed while maintaining accuracy methods. The is open-source freely from: http://github.com/marbl/harvest .

Language: Английский

Citations

1471
Discovery of microbial natural products by activation of silent biosynthetic gene clusters DOI
Peter J. Rutledge, Gregory L. Challis

Nature Reviews Microbiology, Journal Year: 2015, Volume and Issue: 13(8), P. 509 - 523

Published: June 29, 2015

Language: Английский

Citations

858
How important are transposons for plant evolution? DOI
Damon Lisch

Nature Reviews Genetics, Journal Year: 2012, Volume and Issue: 14(1), P. 49 - 61

Published: Dec. 18, 2012

Language: Английский

Citations

840
Genetic variance estimation with imputed variants finds negligible missing heritability for human height and body mass index DOI
Jian Yang, Andrew Bakshi, Zhihong Zhu

et al.

Nature Genetics, Journal Year: 2015, Volume and Issue: 47(10), P. 1114 - 1120

Published: Aug. 31, 2015

Language: Английский

Citations

815
ChIP–seq and beyond: new and improved methodologies to detect and characterize protein–DNA interactions DOI
Terrence S. Furey

Nature Reviews Genetics, Journal Year: 2012, Volume and Issue: 13(12), P. 840 - 852

Published: Oct. 23, 2012

Language: Английский

Citations

786
Completing bacterial genome assemblies with multiplex MinION sequencing DOI Creative Commons
Ryan R. Wick, Louise M. Judd, Claire L. Gorrie

et al.

Microbial Genomics, Journal Year: 2017, Volume and Issue: 3(10)

Published: Sept. 13, 2017

Illumina sequencing platforms have enabled widespread bacterial whole genome sequencing. While data is appropriate for many analyses, its short read length limits ability to resolve genomic structure. This has major implications tracking the spread of mobile genetic elements, including those which carry antimicrobial resistance determinants. Fully resolving a requires long-read such as generated by Oxford Nanopore Technologies (ONT) platforms. Here we describe our use ONT MinION sequence 12 isolates

Language: Английский

Citations

778
Improved data analysis for the MinION nanopore sequencer DOI
Miten Jain, Ian T. Fiddes, Karen H. Miga

et al.

Nature Methods, Journal Year: 2015, Volume and Issue: 12(4), P. 351 - 356

Published: Feb. 16, 2015

Language: Английский

Citations

644
A beginner's guide to eukaryotic genome annotation DOI
Mark Yandell, Daniel Ence

Nature Reviews Genetics, Journal Year: 2012, Volume and Issue: 13(5), P. 329 - 342

Published: April 18, 2012

Language: Английский

Citations

597
Ray Meta: scalable de novo metagenome assembly and profiling DOI Creative Commons
Sébastien Boisvert, Frédéric Raymond,

Élénie Godzaridis

et al.

Genome biology, Journal Year: 2012, Volume and Issue: 13(12)

Published: Dec. 22, 2012

Abstracta Voluminous parallel sequencing datasets, especially metagenomic experiments, require distributed computing for de novo assembly and taxonomic profiling. Ray Meta is a massively metagenome assembler that coupled with Communities, which profiles microbiomes based on uniquely-colored k-mers. It can accurately assemble profile three billion read experiment representing 1,000 bacterial genomes of uneven proportions in 15 hours 1,024 processor cores, using only 1.5 GB per core. The software will facilitate the processing large complex help generating biological insights specific environments. open source available at http://denovoassembler.sf.net .

Language: Английский

Citations

587
TEtranscripts: a package for including transposable elements in differential expression analysis of RNA-seq datasets DOI Open Access

Ying Jin,

Oliver H. Tam,

Eric Paniagua

et al.

Bioinformatics, Journal Year: 2015, Volume and Issue: 31(22), P. 3593 - 3599

Published: July 23, 2015

Abstract Motivation: Most RNA-seq data analysis software packages are not designed to handle the complexities involved in properly apportioning short sequencing reads highly repetitive regions of genome. These often occupied by transposable elements (TEs), which make up between 20 and 80% eukaryotic genomes. They can contribute a substantial portion transcriptomic genomic sequence reads, but typically ignored most analyses. Results: Here, we present method package for including both gene- TE-associated ambiguously mapped differential expression analysis. Our shows improved recovery TE transcripts over other published methods, synthetic qPCR/NanoString-validated datasets. Availability implementation: The source code, associated GTF files annotation, testing freely available at http://hammelllab.labsites.cshl.edu/software. Contact: [email protected]. Supplementary information: Bioinformatics online.

Language: Английский

Citations

573