scholarly journals A rapid and simple method for assessing and representing genome sequence relatedness

2021 ◽  
Vol 1 ◽  
pp. 1-None
Author(s):  
M Briand ◽  
M Bouzid ◽  
G Hunault ◽  
M Legeay ◽  
M Fischer-Le Saux ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Simple Method ◽  
Sequence Relatedness

scholarly journals Coverage-versus-Length plots, a simple quality control step for de novo yeast genome sequence assemblies

2018 ◽  
Author(s):  
Alexander P. Douglass ◽  
Caoimhe E. O’Brien ◽  
Benjamin Offei ◽  
Aisling Y. Coughlan ◽  
Raúl A. Ortiz-Merino ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genome Assembly ◽  
De Novo ◽  
Yeast Genome ◽  
Coverage Level ◽  
Microsoft Excel ◽  
Simple Method ◽  
A Genome ◽  
Low Coverage ◽  
Yeast Genomes

AbstractIllumina sequencing has revolutionized yeast genomics, with prices for commercial draft genome sequencing now below $200. The popular SPAdes assembler makes it simple to generate a de novo genome assembly for any yeast species. However, whereas making genome assemblies has become routine, understanding what they contain is still challenging. Here, we show how graphing the information that SPAdes provides about the length and coverage of each scaffold can be used to investigate the nature of an assembly, and to diagnose possible problems. Scaffolds derived from mitochondrial DNA, ribosomal DNA, and yeast plasmids can be identified by their high coverage. Contaminating data, such as cross-contamination from other samples in a multiplex sequencing run, can be identified by its low coverage. Scaffolds derived from the bacteriophage PhiX174 and Lambda DNAs that are frequently used as molecular standards in Illumina protocols can also be detected. Assemblies of yeast genomes with high heterozygosity, such as interspecies hybrids, often contain two types of scaffold: regions of the genome where the two alleles assembled into two separate scaffolds and each has a coverage level C, and regions where the two alleles co-assembled (collapsed) into a single scaffold that has a coverage level 2C. Visualizing the data with Coverage-versus-Length (CVL) plots, which can be done using Microsoft Excel or Google Sheets, provides a simple method to understand the structure of a genome assembly and detect aberrant scaffolds or contigs. We provide a Python script that allows assemblies to be filtered to remove contaminants identified in CVL plots.100-word article summaryWe describe a simple new method, Coverage-versus-Length plots, for examining de novo genome sequence assemblies. These plots enable researchers to detect scaffolds that have unusually high or unusually low coverage, which allows contaminants, and scaffolds that come from atypical parts of the organism’s DNA complement, to be detected. We show that contaminants are common in yeast genomes sequenced in multiplex Illumina runs. We provide instructions for making plots using Microsoft Excel or Google Sheets, and software for filtering assemblies to remove contaminants. Contaminants can be detected and removed, even without knowing their source.

scholarly journals A rapid and simple method for assessing and representing genome sequence relatedness

2019 ◽  
Author(s):  
M Briand ◽  
M Bouzid ◽  
G Hunault ◽  
M Legeay ◽  
M Fischer-Le Saux ◽  
...  
Keyword(s):  
Circle Packing ◽  
Bacterial Species ◽  
Genomic Sequences ◽  
Species Delineation ◽  
Genome Sequences ◽  
Simple Method ◽  
Computationally Intensive ◽  
Sequence Relatedness ◽  
User Friendly

AbstractCoherent genomic groups are frequently used as a proxy for bacterial species delineation through computation of overall genome relatedness indices (OGRI). Average nucleotide identity (ANI) is a widely employed method for estimating relatedness between genomic sequences. However, pairwise comparisons of genome sequences based on ANI is relatively computationally intensive and therefore precludes analyses of large datasets composed of thousands of genome sequences.In this work we proposed a workflow to compute and visualize relationships between genomic sequences. A dataset containing more than 3,500 Pseudomonas genome sequences was successfully classified with an alternative OGRI based on k-mer counts in few hours with the same precision as ANI. A new visualization method based on zoomable circle packing was employed for assessing relationships among the 350 groups generated. Amendment of databases with these Pseudomonas groups greatly improved the classification of metagenomic read sets with k-mer-based classifier.The developed workflow was integrated in the user-friendly KI-S tool that is available at the following address:https://iris.angers.inra.fr/galaxypub-cfbp.

A simple way for producing holographic filters suitable for image improvement

1978 ◽  
Vol 36 (1) ◽  
pp. 226-227
Author(s):  
K.-H. Herrmann ◽  
E. Reuber ◽  
P. Schiske
Keyword(s):  
Transfer Functions ◽  
Diffraction Order ◽  
Lateral Position ◽  
Simple Method ◽  
Spatial Frequencies ◽  
Resolution Electron ◽  
Wiener Filters ◽  
Image Improvement ◽  
Optical Reconstruction ◽  
Set Up

Aposteriori deblurring of high resolution electron micrographs of weak phase objects can be performed by holographic filters [1,2] which are arranged in the Fourier domain of a light-optical reconstruction set-up. According to the diffraction efficiency and the lateral position of the grating structure, the filters permit adjustment of the amplitudes and phases of the spatial frequencies in the image which is obtained in the first diffraction order.In the case of bright field imaging with axial illumination, the Contrast Transfer Functions (CTF) are oscillating, but real. For different imageforming conditions and several signal-to-noise ratios an extensive set of Wiener-filters should be available. A simple method of producing such filters by only photographic and mechanical means will be described here.A transparent master grating with 6.25 lines/mm and 160 mm diameter was produced by a high precision computer plotter. It is photographed through a rotating mask, plotted by a standard plotter.

Rotary Beveling for In Situ Thin-Section Microscopy of Cell Cultures

1981 ◽  
Vol 39 ◽  
pp. 550-551
Author(s):  
Dean A. Handley ◽  
Jack T. Alexander ◽  
Shu Chien
Keyword(s):  
Cell Growth ◽  
Cell Cultures ◽  
Molecular Interactions ◽  
Convenient Method ◽  
Petri Dish ◽  
Simple Method ◽  
Thin Section Microscopy ◽  
Thin Sectioning ◽  
Organic Fluids

In situ preparation of cell cultures for ultrastructural investigations is a convenient method by which fixation, dehydration and embedment are carried out in the culture petri dish. The in situ method offers the advantage of preserving the native orientation of cell-cell interactions, junctional regions and overlapping configurations. In order to section after embedment, the petri dish is usually separated from the polymerized resin by either differential cryo-contraction or solvation in organic fluids. The remaining resin block must be re-embedded before sectioning. Although removal of the petri dish may not disrupt the native cellular geometry, it does sacrifice what is now recognized as an important characteristic of cell growth: cell-substratum molecular interactions. To preserve the topographic cell-substratum relationship, we developed a simple method of tapered rotary beveling to reduce the petri dish thickness to a dimension suitable for direct thin sectioning.

Development of a simple method for the determination of single nucleotide polymorphisms

2010 ◽  
Vol 34 (8) ◽  
pp. S75-S75
Author(s):  
Weifeng Zhu ◽  
Zhuoqi Liu ◽  
Daya Luo ◽  
Xinyao Wu ◽  
Fusheng Wan
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Nucleotide Polymorphisms ◽  
Simple Method ◽  
Single Nucleotide
Sign in / Sign up

Export Citation Format

Share Document