BOL: Related items

Genome sequence-based (sub-)species delineation.

Abhimanyu Singh — Wed, 12 Dec 2018 08:31:14 -0600

The GGDC web service reports digital DDH for a universal and accurate delineation of prokaryotic (sub-)species without inheriting the pitfalls of classic DDH, and also calculates differences in genomic G+C content.

http://ggdc.dsmz.de/ggdc_background.php#

Genome-to-Genome Distance Calculator 2.1

http://ggdc.dsmz.de/ggdc.php

Address of the bookmark: http://ggdc.dsmz.de/

KAU Thrissur Biotech/Bioinformatics RA/SRF/JRF/Trainee/Studentships

Fri, 26 Sep 2014 20:07:28 -0500

Applications are invited from eligible candidates for the following posts at Bioinformatics Centre (DIC), IT- BT Complex, College of Horticulture, Kerala Agricultural University, Vellanikkara, Thrissur.

1. Research Associate
Emoluments*: 14880/- + HRA
Qualification needed: Ph.D/M.Sc in Bioinformatics or Ph.D/M.Sc in Agriculture or Biotechnology with advanced Diploma in Bioinformatics
Desirable: 2 year experience in Bioinformatics.

2 Senior Research Fellow
Emoluments*: 10230/-
Qualification needed: M.Sc/ M.tech in Bioinformatics or M.Sc in Agriculture/ Biotechnology with Diploma in Bioinformatics.
Desirable: One year experience in Bioinformatics

3 Junior Research Fellow
Emoluments*: 9300/-
Qualification needed: M.Sc/ M.tech in Bioinformatics or M.Sc in Agriculture/Biotechnology/Plant Sciences with Diploma in Bioinformatics.

4 .Trainee/Studentship Bioinformatics
Emoluments*: 5000/-
Qualification needed: M.Sc in Bioinformatics with good knowledge of Bioinformatics softwares and tools.

5 Trainee/ Studentship Biotechnology
Emoluments*: 5000/-
Qualification needed: M.Sc in Biotechnology, with working knowledge in tissue culture, molecular markers and cloning of genes.

Candidates with the required qualifications and experience may give an application in the prescribed format with attested copies of certificates to prove eligibility on or before 30th November 2014. The applications are to be addressed to The Associate Dean, College of Horticulture and send to "Professor & Coordinator, Bioinformatics Centre (DIC), IT-BT Complex, Kerala Agricultural University, Vellanikkara, Thrissur, Kerala 680 656”. The envelope may be superscribed “Application for the post at Bioinformatics Centre”.

*Emoluments are likely to be revised in 2014-2015

More at http://www.kaubic.in/downloads/Notification_bic.pdf
http://www.kaubic.in/downloads/Application%20form.pdf

Roary: the Pan Genome Pipeline

Jit — Tue, 22 Jan 2019 05:52:07 -0600

Roary is a high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome. Using a standard desktop PC, it can analyse datasets with thousands of samples, something which is computationally infeasible with existing methods, without compromising the quality of the results. 128 samples can be analysed in under 1 hour using 1 GB of RAM and a single processor. To perform this analysis using existing methods would take weeks and hundreds of GB of RAM. Roary is not intended for meta-genomics or for comparing extremely diverse sets of genomes.

Address of the bookmark: https://sanger-pathogens.github.io/Roary/

FACULTY POSITION at NATIONAL INSTITUTE OF TECHNOLOGY, ROURKELA

Sun, 05 Oct 2014 15:45:13 -0500

NIT, Rourkela, an institute of national importance under Ministry of HRD, Govt. of India invites applications from Indian nationals possessing excellent academic background along with commitment to quality teaching and research for faculty positions at the level of Professor, Associate Professor and Assistant Professor in most branches of Engineering, Science, Management and Humanities as per following table:-

1 Asst. Professor (on Pre-Ph.D. Contract)

2 Asst. Professor (on Contract)

3 Asst. Professor

4 Associate Professor

5 Professor

Life Sciences:-

i)Biochemistry and Molecular Biology; ii)Cell and Developmental Biology; iii)Immunology and Molecular Medicine; (iv) Microbiology and Ecology (v)Bioinformatics Group; vi)Biophysical Sciences

HOW TO APPLY:-

a. Candidates willing to apply for one or more posts are requested to apply online at “http://www.nitrkl.ac.in/ JOBS & TENDERS /Faculty Position” .
b. Persons employed in Government and Semi-Government organizations may apply directly against the standing advertisement. For this the application should be completed online. The printout of the application generated online should be submitted through employer if shortlisted for interview.
c. The online application can be filled in multiple sessions.
d. Candidates are required to check the Institute website from time to time for latest information, application status call for interview, change of dates and final results.
e. Applications shall be received online only. Please do not send application or CV against this advertisement by email or letter mail.

More Info: http://nitrkl.ac.in/Jobs_Tenders/1FacultyPosition/Default.aspx

RaGOO: Fast Reference-Guided Scaffolding of Genome Assembly Contigs

BioJoker — Wed, 17 Apr 2019 19:45:22 -0500

Alonge M, Soyk S, Ramakrishnan S, Wang X, Goodwin S, Sedlazeck FJ, Lippman ZB, Schatz MC: Fast and accurate reference-guided scaffolding of draft genomes. bioRxiv 2019.

RaGOO is a tool for coalescing genome assembly contigs into pseudochromosomes via minimap2 alignments to a closely related reference genome. The focus of this tool is on practicality and therefore has the following features:

Good performance. On a MacBook Pro using Arabidopsis data, pseudochromosome construction takes less than a minute and the whole pipeline with SV calling takes ~2 minutes.
Intact ordering and orienting of contigs.
Chimeric contig correction
GFF lift-over
Structural variant calling with and integrated version of Assemblytics
Confidence scores associated with the grouping, localization, and orientation for each contig.

Address of the bookmark: https://github.com/malonge/RaGOO

Software developed in pevsner lab

Robert M Willioms — Mon, 06 Oct 2014 12:41:26 -0500

DRAGON: Database Referencing of Array Genes Online

SNOMAD: Standardization and Normalization of Microarray Data

SNPduo: SNP Analysis Between Two Individuals

SNPtrio: Analyzing and Visualizing and Inheritance Patterns in Trios

SNPscan: Data Analysis and Visualization of SNP Data

pediSNP: Analyze SNP Data From a Pedigree of Two Generations

kcoeff: Calculate Cotterman Coefficients of SNP Genotype Data

triPOD: Detects chromosomal abnormalities in parent-child trio-based microarray data

Address of the bookmark: http://pevsnerlab.kennedykrieger.org/php/?q=software

MGSE: Mapping-based Genome Size Estimation

Shruti Paniwala — Fri, 17 Jan 2020 02:11:43 -0600

MGSE can harness the power of files generated in genome sequencing projects to predict the genome size. Required are the FASTA file containing a high continuity assembly and a BAM file with all available reads mapped to this assembly. The script construct_cov_file.py (https://doi.org/10.1186/s12864-018-5360-z) allows the generation of a COV file based on the (sorted) BAM file (also possible via MGSE directly). Next, this COV file can be used by MGSE to calculate the coverage in provided reference regions and to calculate the total number of mapped bases. Both values are subjected to the genome size estimation. Providing accurate reference regions is crucial for this genome size estimation.

Address of the bookmark: https://github.com/bpucker/MGSE

Research Fellows at CSIR - Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh

Tue, 19 May 2015 07:17:32 -0500

CSIR - Institute of Himalayan Bioresource Technology 2 vacancies of Project Fellow

Name of the Post: Project Fellow

No. of the Post: 02 Two

Salary: Rs. 12000/- per month or Rs. 14000/- per month

Age Limit: Max. 28 years as on 10.06.2015 and relaxation as per rules

Required Job Profile:

Candidate must possess first class B.Tech. in bioinformatics or computational biology OR M.Sc. in bioinformatics or computational biology with fifty five percent marks OR M.Tech. in bioinformatics or computational biology with fifty five percent marks.

How to apply:

Eligible and interested candidates should need to appear for walk-in interview on 10.06.2015 at 9:00 am at the above mentioned address.

Refer to http://www.ihbt.res.in/recruit/AdvtNo7_2015.pdf

Synteny and Rearrangement Identifier (SyRI)

Jit — Tue, 05 May 2020 10:37:10 -0500

SyRI is a comprehensive tool for predicting genomic differences between related genomes using whole-genome assemblies (WGA). The assemblies are aligned using whole-genome alignment tools, and these alignments are then used as input to SyRI. SyRI identifies syntenic path (longest set of co-linear regions), structural rearrangements (inversions, translocations, and duplications), local variations (SNPs, indels, CNVs etc) within syntenic and structural rearrangements, and un-aligned regions.

Address of the bookmark: https://schneebergerlab.github.io/syri/

Big genomic data on Google Cloud Platform

Fri, 17 Oct 2014 02:16:00 -0500

As the cost of DNA sequencing has dropped, the volume of data produced has risen into the petabytes. Google is working with the genomics community to define a standard API for working with big genomic data sets in the cloud. Building on Google Cloud Platform, we show how to store, process, explore and share genomic data using technologies like BigQuery, AppEngine MapReduce, R and more.