BOL: Related items

The MARVEL assembler

Jit — Fri, 04 May 2018 19:18:41 -0500

MARVEL consists of a set of tools that facilitate the overlapping, patching, correction and assembly of noisy (not so noisy ones as well) long reads.

The assembly process can be summarized as follows:

overlap
patch reads
overlap (again)
scrubbing
assembly graph construction and touring
optional read correction
fasta file creation

Address of the bookmark: https://github.com/schloi/MARVEL

Research Associate Bioinformatics job position in Indian Agricultural Statistics Research Institute (IASRI), Pusa, New Delhi

Tue, 14 Apr 2015 11:57:13 -0500

Indian Agricultural Statistics Research Institute is inviting applications from indian citizens for recruiting following posts:

Vacancies:
Research Associate-02
Age Limits:
Candidates age limit should be not more than 40 years as on date of interview.
Qualification:
Candidates should possess Ph.D in Bioinformatics/Agricultural Statistics/Statistics/Computer Science/Computer Application or equivalent.
Selection Process:
Selection will be based on interview.
How to Apply:
Eligible candidates may attend for interview along with application in prescribed format, recent passport size photograph pasted on the application form, bio-data, original certificates and self attested copies of relevant documents, all experience certificates, testimonials etc, held at Indian Agricultural Statistics Research Institute, Pusa, New Delhi on 18-04-2015 at 10:30 AM.
Last Date:
18-04-2015

GAPPadder: A Sensitive Approach for Closing Gaps on Draft Genomes with Short Sequence Reads

Jit — Mon, 14 May 2018 05:25:48 -0500

This software is provided ``as is” without warranty of any kind. In no event shall the author be held responsible for any damage resulting from the use of this software. The program package, including source codes, executables, and this documentation, is distributed free of charge. If you use this program in a publication, please cite the following reference:
Chong Chu, Xin Li, and Yufeng Wu. "GAPPadder: A Sensitive Approach for Closing Gaps on Draft Genomes with Short Sequence Reads." bioRxiv (2017): 125534.

Address of the bookmark: https://github.com/Reedwarbler/GAPPadder

BINC Sample Question Paper !!!

Jitendra Narayan — Thu, 16 Apr 2015 09:12:39 -0500

BINC sample question paper for round ONE.

CGView - Circular Genome Viewer

Rahul Nayak — Wed, 20 Jun 2018 10:15:57 -0500

CGView is a Java package for generating high quality, zoomable maps of circular genomes. Its primary purpose is to serve as a component of sequence annotation pipelines, as a means of generating visual output suitable for the web. Feature information and rendering options are supplied to the program using an XML file, a tab delimited file, or an NCBI ptt file. CGView converts the input into a graphical map (PNG, JPG, or Scalable Vector Graphics format), complete with labels, a title, legends, and footnotes. In addition to the default full view map, the program can generate a series of hyperlinked maps showing expanded views. The linked maps can be explored using any web browser, allowing rapid genome browsing, and facilitating data sharing. The feature labels in maps can be hyperlinked to external resources, allowing CGView maps to be integrated with existing web site content or databases. For examples of the various output types, see the CGView gallery. http://wishart.biology.ualberta.ca/cgview/gallery.html http://stothard.afns.ualberta.ca/downloads/CCT/index.html https://www.gview.ca/wiki/GView/WebHome https://server.gview.ca/ http://stothard.afns.ualberta.ca/cgview_server/ Paper https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bbx081/4037458

Address of the bookmark: http://wishart.biology.ualberta.ca/cgview/

BINC examination 2015 !!!

Jitendra Narayan — Fri, 17 Apr 2015 03:34:28 -0500

BioInformatics National Certification (BINC) Examination 2015 organized by Department of Biotechnology, Government of India, New Delhi Pondicherry University, Puducherry

National Institute of Biologicals Recruitment 2015

Mon, 27 Apr 2015 19:44:45 -0500

National Institute of Biologicals (NIB), Noida
Job Code: 260415(04)Y

National Institute of Biologicals (NIB), Noida invites applications to recruit on vacant posts of Scientist, Training Officer, Administrative Assistant, Stenographer, Junior Engineer, Computer Operator etc. Applications against these Government Jobs can be submitted on or before 01 July 2015.

NIB Vacancy 2015 Details
1. Scientist Grade III – 06
Qualification: PG degree in the concern field.
Age Limit: 35 Years

2. Junior Scientist – 07
Qualification: M.Sc. in Microbiology / Clinical Microbiology / Biotechnology/ Bioinformatics/ Biochemistry/Bacteriology/Pharmacology/ Serology / Molecular Biology/Physiology from any recognized University with at least 60% marks.
Age Limit: 30 Years

How to Apply: Duly filled-in applications in prescribed application format along with copies of required documents should be reach to: Administrative Officer, National Institute of Biologicals (Ministry of Health & Family Welfare), A-32, Sector-62, Institutional Area, Noida-201309. Click here to obtain application form.

The Last Date to apply to NIB Job is 01 July 2015.

Click here to view details http://nib.gov.in/Advt%20%20%2824.04.2015%29.pdf

pWhatsHap: a parallel, high-performance version of WhatsHap

Jit — Wed, 14 Nov 2018 08:20:27 -0600

Given the potential relevance of efficient haplotyping in several analysis pipelines, we have designed and engineered pWhatsHap, a parallel, high-performance version of WhatsHap. pWhatsHap is embedded in a toolkit developed in Python and supports genomics datasets in standard file formats. Building on WhatsHap, pWhatsHap exhibits the same complexity exploring a number of possible solutions which is exponential in the coverage of the dataset. The parallel implementation on multi-core architectures allows for a relevant reduction of the execution time for haplotyping, while the provided results enjoy the same high accuracy as that provided by WhatsHap, which increases with coverage.

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1170-y

Address of the bookmark: https://bitbucket.org/whatshap/whatshap

Walk-ins for JRF ans SRF post in NIRRH, Mumbai

Thu, 28 May 2015 19:04:57 -0500

Title of project- "EXPLORING THE HINGE AND TRANSMEMBRANE REGION OF HUMAN FSHR FOR DESIGN OF SMALL MOLECULE AND PEPTIDOMIMETIC MODULATORS"
Name of the Post- Junior Research Fellow
No. of vacancy- One
Stipend- Rs. 25000/ +30% HRA
Essential qualification- Candidate should be Post Graduate Degree in Life Sciences / Bioinformatics /Pharmacology/ Chemistry or any other relevant area of Biology or Graduate Degree in Professional Course with NET qualification or Post Graduate Degree in Professional Course.
Desirable- Candidate with Good knowledge of protein structures, docking, MD simulations will be preferred.
Age Limit- Not exceeding 28 Years
Duration of project- Upto May 2018

Title of project- "Analysis of the structures of known antimicrobial peptides using machine learning algorithms and molecular dynamics simulations".
Name of the Post- Senior Research Fellow
No. of vacancy- One
Stipend- Rs. 14000/ +30% HRA
Essential qualification- Candidate should be having M.Sc. degree in Life Sciences / Bioinformatics / Pharmacology/ Chemistry or any other relevant area of Biology and 2 years of research experience.
Desirable- Candidate with Good knowledge of protein structures, docking, MD simulations will be preferred.
Age Limit- Not exceeding 35 Years
Duration of project- Upto April 2016
How to Apply- Interested candidates can download the application form from below mentioned link- http://www.nirrh.res.in/links/BiodataForm.pdf
Candidate must bring the filled up application form along with all the relevant documents in original and one set of attested photocopies of the same and one passport size recent colour photograph.

Ref. - http://www.nirrh.res.in/links/job_jrf-srf.htm

Genome Annotation using MAKER tutorial !

Shruti Paniwala — Thu, 20 Dec 2018 17:39:23 -0600

MAKER is a great tool for annotating a reference genome using empirical and ab initiogene predictions. GMOD, the umbrella organization that includes MAKER, has some nice tutorials online for running MAKER. However, these were quite simplified examples and it took a bit of effort to wrap my head completely around everything. Here I will describe a de novo genome annotation for Boa constrictor in detail, so that there is a record and that it is easy to use this as a guide to annotate any genome.

Address of the bookmark: https://www.biostars.org/p/261203/