BOL: Related items

MeDuSa: a multi-draft based scaffolder

Abhimanyu Singh — Wed, 14 Feb 2018 02:49:00 -0600

MeDuSa (Multi-Draft based Scaffolder), an algorithm for genome scaffolding. MeDuSa exploits information obtained from a set of (draft or closed) genomes from related organisms to determine the correct order and orientation of the contigs. MeDuSa formalises the scaffolding problem by means of a combinatorial optimisation formulation on graphs and implements an efficient constant factor approximation algorithm to solve it. In contrast to currently used scaffolders, it does not require either prior knowledge on the microrganisms dataset under analysis (e.g. their phylogenetic relationships) or the availability of paired end read libraries.

Address of the bookmark: https://github.com/combogenomics/medusa

Porechop: tool for finding and removing adapters from Oxford Nanopore reads

Rahul Nayak — Tue, 29 May 2018 07:33:44 -0500

Porechop is a tool for finding and removing adapters from Oxford Nanopore reads. Adapters on the ends of reads are trimmed off, and when a read has an adapter in its middle, it is treated as chimeric and chopped into separate reads. Porechop performs thorough alignments to effectively find adapters, even at low sequence identity.

Porechop also supports demultiplexing of Nanopore reads that were barcoded with the Native Barcoding Kit, PCR Barcoding Kit or Rapid Barcoding Kit.

Address of the bookmark: https://github.com/rrwick/Porechop

LAPTI Lab

Thu, 12 Dec 2013 18:19:12 -0600

The main theme of our research is the understanding of how genetic information is decoded from DNA into RNA and proteins. Someone may find this topic a little strange and argue that we already know how this is happening.

Translational recoding.

RNA editing.

Evolution of the genetic code and translation.

More at http://lapti.ucc.ie/research.html

Lab page http://lapti.ucc.ie/index.html

Installing Salmon for Trinity !

Rahul Nayak — Tue, 03 Jul 2018 09:02:29 -0500

➜ trinityrnaseq-Trinity-v2.6.6 git:(master) ✗ conda install salmon
Solving environment: done

## Package Plan ##

environment location: /home/urbe/anaconda3

added / updated specs:
- salmon

The following packages will be downloaded:

package | build
---------------------------|-----------------
boost-1.64.0 | py36_4 331 KB conda-forge
jemalloc-5.1.0 | hfc679d8_0 8.2 MB conda-forge
boost-cpp-1.64.0 | 1 17.8 MB conda-forge
salmon-0.10.2 | 1 3.7 MB bioconda
conda-4.5.5 | py36_0 624 KB conda-forge
tbb-2018_20171205 | 0 1.2 MB conda-forge
------------------------------------------------------------
Total: 31.8 MB

The following NEW packages will be INSTALLED:

boost: 1.64.0-py36_4 conda-forge
boost-cpp: 1.64.0-1 conda-forge
jemalloc: 5.1.0-hfc679d8_0 conda-forge
salmon: 0.10.2-1 bioconda
tbb: 2018_20171205-0 conda-forge

The following packages will be UPDATED:

conda: 4.5.4-py36_0 conda-forge --> 4.5.5-py36_0 conda-forge

Proceed ([y]/n)? y

Downloading and Extracting Packages
boost-1.64.0 | 331 KB | ####################################################################################################################################### | 100%
jemalloc-5.1.0 | 8.2 MB | ####################################################################################################################################### | 100%
boost-cpp-1.64.0 | 17.8 MB | ####################################################################################################################################### | 100%
salmon-0.10.2 | 3.7 MB | ####################################################################################################################################### | 100%
conda-4.5.5 | 624 KB | ####################################################################################################################################### | 100%
tbb-2018_20171205 | 1.2 MB | ####################################################################################################################################### | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done

Junior Research Fellow (JRF) / Project Fellow @ Kalasalingam University

Thu, 19 Dec 2013 13:23:39 -0600

Applications are invited from interested candidates for the post of one Junior Research Fellow / Project Fellow on a purely temporary basis in a time bound research project (3 years) sponsored by Science and Engineering Research Board, Government of India, New Delhi.

Name of the fellowship: Junior Research Fellow (JRF) / Project Fellow

Title of the project: Genome-wide Mapping of Murine Specific Dengue T-cell Epitopes: Computational Prediction, Identification and use as Candidate Vaccines

Duration: 3 years

Fellowship: Rs. 18,000 for first 2 years and Rs. 20,000 for 3rdyear (for M.Tech. candidates)

Rs. 16,000 for first 2 years and Rs. 18,000 for 3rdyear (for M.Sc. candidates with NET qualification)

Rs. 8,000 for first 2 years and Rs. 10,000 for 3rdyear (for M.Sc. candidates without NET qualification)

Qualifications: M.Tech. in Biotechnology / M.Sc. in any branch of Life Sciences

Desirable Experience: Minimum of two years research experience in any of the following areas: Immunology / Microbiology / Gene Manipulation / Bioinformatics

Interested and eligible candidates may apply with their resume along with relevant documents and a passport size photograph to the Principal Investigator by post (or e-mail) on or before December 31, 2013. Only short listed candidates will be called for written test and/or interview. Selected candidate may register for PhD in Kalasalingam University. No TA/DA will be paid for attending interview.

Dr. K. Sundar
Principal Investigator (SERB Project)
Department of Biotechnology
Kalasalingam University
Krishnankoil – 626126, Tamil Nadu
sundarkr@klu.ac.in

List of non-commercial NGS genotype-calling software

Jit — Thu, 09 Aug 2018 04:21:32 -0500

Meaningful analysis of next-generation sequencing (NGS) data, which are produced extensively by genetics and genomics studies, relies crucially on the accurate calling of SNPs and genotypes. Recently developed statistical methods both improve and quantify the considerable uncertainty associated with genotype calling, and will especially benefit the growing number of studies using low- to medium-coverage data.

A list of programs for genotype and SNP calling :

SOAP2 http://soap.genomics.org.cn/index.html

Single-sample High-quality variant database (for example, dbSNP) Package for NGS data analysis, which includes a single individual genotype caller (SOAPsnp)

realSFS http://128.32.118.212/thorfinn/realSFS/

Single-sample Aligned reads Software for SNP and genotype calling using single individuals and allele frequencies. Site frequency spectrum (SFS) estimation

Samtools http://samtools.sourceforge.net/

Multi-sample Aligned reads Package for manipulation of NGS alignments, which includes a computation of genotype likelihoods (samtools) and SNP and genotype calling (bcftools)

GATK http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit Multi-sample Aligned reads Package for aligned NGS data analysis, which includes a SNP and genotype caller (Unifed Genotyper), SNP filtering (Variant Filtration) and SNP quality recalibration (Variant Recalibrator)

Beagle http://faculty.washington.edu/browning/beagle/beagle.html

Multi-sample LD Candidate SNPs, genotype likelihoods Software for imputation, phasing and association that includes a mode for genotype calling

IMPUTE2 http://mathgen.stats.ox.ac.uk/impute/impute_v2.html

Multi-sample LD Candidate SNPs, genotype likelihoods Software for imputation and phasing, including a mode for genotype calling. Requires fine-scale linkage map

QCall ftp://ftp.sanger.ac.uk/pub/rd/QCALL

Multi-sample LD ‘Feasible’ genealogies at a dense set of loci, genotype likelihoods Software for SNP and genotype calling, including a method for generating candidate SNPs without LD information (NLDA) and a method for incorporating LD information (LDA). The ‘feasible’ genealogies can be generated using Margarita (http://www.sanger.ac.uk/resources/software/margarita)

MaCH http://genome.sph.umich.edu/wiki/Thunder

Multi-sample LD Genotype likelihoods Software for SNP and genotype calling, including a method (GPT_Freq) for generating candidate SNPs without LD information and a method (thunder_glf_freq) for incorporating LD information

Asst. Professor @ JAIPUR NATIONAL UNIVERSITY

Fri, 27 Dec 2013 19:54:40 -0600

JAIPUR NATIONAL UNIVERSITY

Established by Government of Rajasthan

Approved by UGC under Sec 2(f) of UGC Act 1956

ADVERTISEMENT FOR FACULTY POSITION AT JAIPUR NATIONAL UNIVERSITY,JAIPUR

Jaipur National University, Jaipur is a premier centre of learning, providing various integrated and interdisciplinary programmes of study and research in the country. With the opening of the School of Distance Education & Learning, JNU has taken education to the doorsteps of those aspirants who, for some reason, could not be a part of regular stream of education. In this era of competition & ambition for excellence, it has become imperative to have quality education & an alert mind coupled with the right attitude to carry onself, and for this, JNU happens to be the most sought after destination.

School Of Life Sciences: Bioinformatics, Chemistry

Total no of Post: 04

Education:

PG – M.Sc /M.Tech Bioinformatics

PG – M.Sc /M.Tech Chemistry

Experience:

Candidate with 1-2 years of teaching experience in college/ University will be preffered. Freshers may also apply.

Compensation: Compensation will not be a problem for the right candidate

HOW TO APPLY:

SEND THE UPDATED RESUME THROUGH MAIL OR POST AT

dsbhatia5@yahoo.com

contact no: 7568246839

Website: http://www.jnujaipur.ac.in

Please mail your resume to Prof.D.S.Bhatia

Email Address: dsbhatia5@yahoo.com

Ph:, +917568246839

You can't hide from Genome Hackers

Neel — Sat, 13 Oct 2018 14:17:28 -0500

Young computational biologist named Yaniv Erlich shocked the research world by showing it was possible to unmask the identities of people listed in anonymous genetic databases using only an Internet connection

Paper: http://science.sciencemag.org/content/early/2018/10/10/science.aau4832

More at https://www.wired.com/story/genome-hackers-show-no-ones-dna-is-anonymous-anymore/

SENIOR PROGRAMMER @ Biotech Park

Mon, 20 Jan 2014 04:50:36 -0600

Advt. No. (1)/BP/2014
A walk-in-interview will be held in the Biotech Park Office at Sector G, Jankipuram, Kursi Road, Lucknow (U.P.) January 31, 2014 at 11.00 A.M. for the following posts of DBT sponsored project tenable at Biotech Park. Interested candidates fulfilling the requisite qualifications, experience and age as given below, on the date of interview, may appear before the Selection Committee. The candidate will have to join immediately. Appointment will be made initially for six months extendable on satisfactory performance till the duration of the project.
INTERVIEW ON January 31, 2014 at 11.00 A.M.

SENIOR PROGRAMMER (ONE POST)
Educational Qualification
M.Sc./B. Tech Bioinformatics with minimum 60% marks with two years of relevant experience
Job Requirement
Development of databases in multi user environment and application softwares, updating and maintenance of website, Drug designing and QSAR study etc.
Desirable
Knowledge of Bioinformatics tools, Windows, Linux, C++, JAVA / JAVA Script, Visual Basic, CGI, DBMS/RDBMS and HTML. Experience in various domains of bioinformatics such as structure based drug designing, Newtonian dynamics and QSAR studies.
Age
Below 35 years (as on the date of interview)
Emoluments
Rs. 12,000/- per month fixed.
Note: All the candidates should report for interview on or before 10.30 A.M
General Conditions
The aforesaid positions are purely temporary and do not give the incumbent any right whatsoever for appointment on regular basis.
The applicant will have to submit typed and duly signed application on plain paper on the day of interview stating:
(a) Advertisement No.
(b) Position applied for
(c) Name of Applicant (in Block letters)
(d) Father’s Name
(e) Date of Birth
(f) Sex
(g) Age as on the date of interview (dd / mm / yy )
(h) Address (Permanent & correspondence)
(i) Educational Qualifications (High School onwards) with examination passed, year, % marks, subjects
(j) Employment experience, if any i.e. Name of employer, nature of employment, date of joining and leaving.
Applications must be accompanied by a latest passport size photograph and attested copies of certificates
Original certificates/degree and testimonials should be produced by the candidate for verification at the time of interview.

Tenure: Initially upto six months and extendable based on performance.
The upper age limit can be relaxed up to 5 years in the case of applicant belonging to SC/ST/Woman/Physically handicapped and 3 years for OBCs.
No TA/DA will be paid for attending the interview.
More at http://www.biotechpark.org.in/index1.htm

Genobuntu: A software package containing more than 70 software and packages oriented towards NGS and genome assembly

BioStar — Tue, 11 Dec 2018 05:15:57 -0600

Genobuntu is a software package containing more than 70 software and packages oriented towards NGS. In its current version, Genobuntu supports pre assembly tools, genome assemblers as well as post assembly tools.

Commonly used biological software and example script files for different assembly pipelines have also been provided, where the example script files can be updated to suit one’s experimental needs. Genobuntu attempts to reduce the amount of time and energy needed to build software workstations and it can also act as a good teaching source for a class room setting.

https://sourceforge.net/projects/genobuntu/

Address of the bookmark: https://sourceforge.net/projects/genobuntu/