BOL: Related items

ALLHiC: Phasing and scaffolding polyploid genomes based on Hi-C data

BioStar — Thu, 20 Dec 2018 12:03:32 -0600

The major problem of scaffolding polyploid genome is that Hi-C signals are frequently detected between allelic haplotypes and any existing stat of art Hi-C scaffolding program links the allelic haplotypes together. To solve the problem, we developed a new Hi-C scaffolding pipeline, called ALLHIC, specifically tailored to the polyploid genomes. ALLHIC pipeline contains a total of 5 steps: prune, partition, rescue, optimize and build.

Address of the bookmark: https://github.com/tangerzhang/ALLHiC/wiki

SvABA: Genome-wide detection of structural variants and indels by local assembly

Abhimanyu Singh — Mon, 21 Jan 2019 17:58:56 -0600

SvABA is a method for detecting structural variants in sequencing data using genome-wide local assembly. Under the hood, SvABA uses a custom implementation of SGA (String Graph Assembler) by Jared Simpson, and BWA-MEM by Heng Li. Contigs are assembled for every 25kb window (with some small overlap) for every region in the genome. The default is to use only clipped, discordant, unmapped and indel reads, although this can be customized to any set of reads at the command line using VariantBam rules. These contigs are then immediately aligned to the reference with BWA-MEM and parsed to identify variants. Sequencing reads are then realigned to the contigs with BWA-MEM, and variants are scored by their read support.

Address of the bookmark: https://github.com/walaj/svaba

TRITEX sequence assembly pipeline for Triticeae genomes

Jit — Tue, 20 Aug 2019 09:47:14 -0500

The pipeline is open-source and hosted in a public Bitbucket repository.

TRITEX has been run on highly inbred genotypes of barley (Hordeum vulgare), tetraploid wheat (Triticum turgidum) and hexaploid wheat (T. aestivum) with reasonable results: super-scaffold N50 values in the range of dozens of Mb and pseudomolecules with better gene space representation than a BAC-by-BAC assembly. It has never been tested and is not expected to work on heterozygous or autopolyploid genomes.

A protocol for generating chromosome-conformation capture sequencing (Hi-C) data suitable for use with the pipeline is described in Himmelbach et al. 2018. Refer to the technical notes of 10X Genomics on how to generate Chromium data.

Address of the bookmark: https://tritexassembly.bitbucket.io/

Randomness and Probability

Jit — Tue, 08 Nov 2016 07:17:32 -0600

Randomness and Probability

Randomness and probability are two differnet concepts: probaility is a measure (according to measure theory) which measures the randomness. Randomness is the object to be measured by probability. For example, probability is a mapping from randomness to the real number between 0 and 1. The similar examples are that the entropy measures the uncertanity; product of length and width measures the area of rectangle etc.

Please see “A mathematical theory of ability measure” by N. Kong ets for more examples to answer this question.

Method in Comparative genomics !!

Jit — Wed, 09 Nov 2016 16:29:24 -0600

We present methods for the automatic determination of genome correspondence. The algorithms enabled the automatic identification of orthologs for more than 90% of genes and intergenic regions across the four species despite the large number of duplicated genes in the yeast genome. The remaining ambiguities in the gene correspondence revealed recent gene family expansions in regions of rapid genomic change.

We present methods for the identification of protein-coding genes based on their patterns of nucleotide conservation across related species. We observed the pressure to conserve the reading frame of functional proteins and developed a test for gene identification with high sensitivity and specificity. We used this test to revisit the genome of S. cerevisiae, reducing the overall gene count by 500 genes (10% of previously annotated genes) and refining the gene structure of hundreds of genes. We present novel methods for the systematic de novo identification of regulatory motifs. The methods do not rely on previous knowledge of gene function and in that way differ from the current literature on computational motif discovery. Based on the genome-wide conservation patterns of known motifs, we developed three conservation criteria that we used to discover novel motifs. We used an enumeration approach to select strongly conserved motif cores, which we extended and collapsed into a small number of candidate regulatory motifs. These include most previously known regulatory motifs as well as several noteworthy novel motifs. The majority of discovered motifs are enriched in functionally related genes, allowing us to infer a candidate function for novel motifs.

Our results demonstrate the power of comparative genomics to further our understanding of any species. Our methods are validated by the extensive experimental knowledge in yeast, and will be invaluable in the study of complex genomes like that of human.

Address of the bookmark: http://web.mit.edu/manoli/www/publications/Kellis_JCB_04.pdf

Supernova: generates phased, whole-genome de novo assemblies from a Chromium-prepared library.

Jit — Sun, 31 May 2020 01:59:30 -0500

Supernova generates phased, whole-genome de novo assemblies from a Chromium-prepared library.

Please see Achieving Success with De Novo Assembly and System Requirements before creating your Chromium libraries for assembly.

Supernova should be run using 38-56x coverage of the genome.
• Somewhat higher coverage is sometimes advantageous.
• Supernova will exit if it finds that coverage is far from the recommended range.
• Note that at most 2.14 billion reads are allowed.
• Please note that we have not extensively tested genomes larger than human, and any genome above approximately 4 GB should be considered experimental and is not supported.

Address of the bookmark: https://support.10xgenomics.com/de-novo-assembly/software/pipelines/latest/using/running

RA Bioinformatics at School of Computational & Integrative Sciences, JNU, India

Fri, 18 Nov 2016 03:57:56 -0600

School of Computational & Integrative Sciences
Jawaharlal Nehru University
New Delhi – 110067

Date: Nov 11th. 2016 Last Date: Nov 25th. 2016

PROJECT ID: 632

The following posts are urgently required to be filled for the Department of Biotechnology, Government of India funded project entitled "Computational Core for Plant Metabolomics" administrated by Prof Indira Ghosh, School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi-110 067

NB:For all Bioinformatics posts, preference will be given to candidates with a good knowledge of Python and/or R. Knowledge of JAVA will also get a special consideration.

RA / Research Associate (Metabolic engineering/Computational Biologist)

Salary: Rs. 36000/- + HRA
Vacancy: 1
Essential Qualifications: PhD in Bioinformatics /Mathematics/Computer Science with experience in analyzing high throughput omics-based data/ system Biology/ Analysis of Network Biology. Published paper in the field is a must to prove the experience.
Desired Skills: Prior experience in handling and guiding bioinformatics, metabolomics data, planning of new research area in metabolic driven network , managing the project portal, preparing and filing reports etc. Will be expected to communicate with user groups and coordinate with LIMS group in Hyderabad and the Cheminformatics group in Delhi.

RA / Research Associate (Chemo-informatics/Computational Biologist)

Salary: Rs. 36000/- + HRA
Vacancy: 1
Essential Qualifications: PhD in Bioinformatics/ computational biology/ Biophysics/Computer Science. Computational and Chemical structure related experience is a necessary qualification proven by paper published and program developed.
Desired Skills: Research experience in Chemical scaffold mapping, in silico Spectral analysis, Biological Database Designing & Integration is required. Individual is responsible to develop methods related to metabolite identification, Testing and refining and integrate LIMS with IIIT Hyderabad and will be expected to communicate with user groups.

Project SRF (Bioinformatics/Programming)

Salary: As per DBT rules
Vacancy: 1
Essential Qualifications: Masters/B Tech in Basic Sciences with at least 2yrs of research experience in Bioinformatics/Computational Biology related to Database /portal building & maintenance ,high throughput data handling and analysis etc. For M.Sc/B.Tec, Published paper in peer-reviewed Journal and for M.Tech, thesis submission in computational biology is a must.

More at http://www.jnu.ac.in/Career/currentjobs.htm

GoJS

Jit — Tue, 22 Nov 2016 08:25:37 -0600

GoJS is a feature-rich JavaScript library for implementing custom interactive diagrams and complex visualizations across modern web browsers and platforms. GoJS makes constructing JavaScript diagrams of complex nodes, links, and groups easy with customizable templates and layouts.

GoJS offers many advanced features for user interactivity such as drag-and-drop, copy-and-paste, in-place text editing, tooltips, context menus, automatic layouts, templates, data binding and models, transactional state and undo management, palettes, overviews, event handlers, commands, and an extensible tool system for custom operations.

GoJS is pure JavaScript, so users get interactivity without requiring round-trips to servers and without plugins. GoJS normally runs completely in the browser, rendering to an HTML5 Canvas element or SVG without any server-side requirements. GoJS does not depend on any JavaScript libraries or frameworks, so it should work with any HTML or JavaScript framework or with no framework at all.

More at http://gojs.net/latest/index.html

Address of the bookmark: http://gojs.net/latest/index.html

auN: a new metric to measure assembly contiguity

Jit — Tue, 02 Aug 2022 01:18:47 -0500

Given a de novo assembly, we often measure the “average” contig length by N50. N50 is neither the real average nor median. It is the length of the contig such that this and longer contigs cover at least 50% of the assembly. A longer N50 indicates better contiguity. We can similarly define Nx such that contigs no shorter than Nx covers x% of the assembly. The Nx curve plots Nx as a function of x, where x is ranged from 0 to 100.

Address of the bookmark: https://lh3.github.io/2020/04/08/a-new-metric-on-assembly-contiguity

Gene Synteny Database

Jit — Fri, 16 Dec 2016 11:09:39 -0600

Comparative genomics remains a pivotal strategy to study the evolution of gene organization, and this primacy is reinforced by the growing number of full genome sequences available in public repositories. Despite this growth, bioinformatic tools available to visualize and compare genomes and to infer evolutionary events remain restricted to two or three genomes at a time, thus limiting the breadth and the nature of the question that can be investigated. Here we present Genomicus, a new synteny browser that can represent and compare unlimited numbers of genomes in a broad phylogenetic view. In addition, Genomicus includes reconstructed ancestral gene organization, thus greatly facilitating the interpretation of the data.

Availability: Genomicus is freely available for online use at http://www.dyogen.ens.fr/genomicus while data can be downloaded at ftp://ftp.biologie.ens.fr/pub/dyogen/genomicus

Contact: rf.sne.eigoloib@crh

Address of the bookmark: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2853686/