BOL: Related items

Studentship at Nagaland University

Tue, 16 Dec 2014 01:35:00 -0600

Nagaland University
(A Central University Estd. By the Act of Parliament No. 35 of 1989)
Lumami 798 627, Nagaland
DBT Sponsored ‘Bioinformatics Infrastructure Facility’ Centre

Applications in plain paper are invited for the posts of (1) Traineeship (2 Nos.) and (2) Studentship – (2 Nos.) in the DBT funded-Bioinformatics Infrastructure Facility (BIF), Nagaland University, Lumami-798627, Nagaland. Details are given below. Interested candidates may submit the application along with self attested copies of certificates in support of the candidature to Prof. Chitta Ranjan Deb, Coordinator or Dr. L. N. Kakati, Deputy Coordinator, BIF Centre, Nagaland University, Lumami-798627, Nagaland on or before 15th January 2015.

The scanned application with relevant documents may be sent by email attachment to bifnulumami@gmail.com. Shortlisted candidates will be informed by email if called for interview. No TA/DA is admissible for attending the interview.

Traineeship (Two nos.)

Post Graduate degree in any branch of Life Sciences from UGC recognized Universities

Knowledge of computers and bioinformatics

Rs.8000/- p.m. fixed.

6 months

Studentship (Two nos.)

Pursuing Post Graduate degree in any branch of Life Sciences from UGC recognized Universities

Knowledge of computers and bioinformatics

Rs.8000/- p.m. fixed.

6 months

Terms and Conditions:

i) Applicants need to produce all original documents if call for interview.
ii) The posts are purely temporary and the appointment does not confer any entitlement or right over the job and will not be considered as formal service.
iii) No TA & DA will be paid for appearing in the walk-in-interview.
iv) The stipend/salary amount is subject to the sanction of DBT, New Delhi.

Advertisement: http://www.nagauniv.org.in/files/BIF%20Advt.pdf

HALC: High throughput algorithm for long read error correction

Jit — Fri, 08 Jun 2018 10:47:41 -0500

HALC, a high throughput algorithm for long read error correction. HALC aligns the long reads to short read contigs from the same species with a relatively low identity requirement so that a long read region can be aligned to at least one contig region, including its true genome region’s repeats in the contigs sufficiently similar to it (similar repeat based alignment approach) HALC was able to obtain 6.7-41.1% higher throughput than the existing algorithms while maintaining comparable accuracy. The HALC corrected long reads can thus result in 11.4-60.7% longer assembled contigs than the existing algorithms.

Address of the bookmark: https://github.com/lanl001/halc

Senior Scientist (Agricultural Bio-informatics) (One post)

Wed, 24 Dec 2014 05:01:02 -0600

Agricultural Scientists Recruitment Board

Qualifications Essential:
Doctoral degree in Bio-informatics/ Biotechnology/Molecular Biology and Biotechnology/Life Sciences/ Computer Sciences with specialization in Bio-informatics including relevant basic sciences with 8 years’ experience in the relevant subject as Scientist/Lecturer or in an equivalent position in the Pay Band- 3 of 15600-39100 with Grade Pay of 5400/6000/7000/8000 having made contribution to research/teachin/extension education as evidenced by published work/innovations and impact.

Doctoral degree in the above subject(s) including relevant basic sciences with minimum 8 years’ experience of high quality post-doctoral research in an institution/organization as evidenced by at least 6 publications in journals with NAAS rating of 7.5 or above.

Desirable:
(i) Specialization and experience: Knowledge of software development and its application in crop bioinformatics, experience in handling ‘omies’data.
(ii) Teaching experience in relevant subject

The Secretary, Agricultural Scientists Recruitment Board, Indian Council of Agricultural Research Krishi Anusandhan Bhavan-I, Pusa New Delhi –110 012, India

Detailed eligibility criteria with how to apply information can be had at:
http://www.indiastudychannel.com/jobs/333467-Indian-Council-of-Agricultural-Research-looking-for-Assistant-Director-General.aspx

More at http://asrb.org.in/administrator/uploads_dir/1418978057english.pdf

nanofilt: Filtering and trimming of long read sequencing data

Jit — Mon, 30 Jul 2018 12:01:52 -0500

Filtering on quality and/or read length, and optional trimming after passing filters.
Reads from stdin, writes to stdout.

Intended to be used:

directly after fastq extraction
prior to mapping
in a stream between extraction and mapping

https://github.com/wdecoster/nanofilt

Address of the bookmark: https://github.com/wdecoster/nanofilt

RStudio

Jitendra Narayan — Sat, 27 Dec 2014 06:50:58 -0600

RStudio IDE is a powerful and productive user interface for R. It’s free and open source, and works great on Windows, Mac, and Linux.

The developers and expert trainers are the authors of several popular R packages, including ggplot2, plyr, lubridate, and others.

More at http://www.rstudio.com/

http://www.rstudio.com/products/RStudio/

Address of the bookmark: http://www.rstudio.com/

BASE: a practical de novo assembler for large genomes using long NGS reads

Rahul Nayak — Fri, 19 Oct 2018 07:25:21 -0500

new de novo assembler called BASE. It enhances the classic seed-extension approach by indexing the reads efficiently to generate adaptive seeds that have high probability to appear uniquely in the genome. Such seeds form the basis for BASE to build extension trees and then to use reverse validation to remove the branches based on read coverage and paired-end information, resulting in high-quality consensus sequences of reads sharing the seeds. Such consensus sequences are then extended to contigs.

Address of the bookmark: https://github.com/dhlbh/BASE

nQuire: A statistical framework for ploidy estimation using NGS short-read data

Jit — Thu, 31 Jan 2019 05:12:19 -0600

nQuire implements a set of commands to estimate ploidy level of individuals from species, where recent polyploidization occurred and intraspecific ploidy variation is observed. Specifically, nQuire uses next-generation sequencing data to distinguish between diploids, triploids and tetraploids, on the basis of frequency distributions at variant sites where only two bases are segregating.

For more background see also the publication at BMC Bioinformatics.

https://github.com/clwgg/nQuire

Address of the bookmark: https://github.com/clwgg/nQuire

Research Associate @ TATA MEMORIAL CENTRE ADVANCED CENTRE FOR TREATMENT, RESEARCH AND EDUCATION IN CANCER KHARGHAR, NAVI MUMBAI

Thu, 08 Jan 2015 20:53:57 -0600

TATA MEMORIAL CENTRE ADVANCED CENTRE FOR TREATMENT, RESEARCH AND EDUCATION IN CANCER KHARGHAR, NAVI MUMBAI – 410210

Website: www.actrec.gov.in; Ph: 27405000

No. ACTREC/Advt./ 66 /2014 23rd December, 2014
Research Associate

International Cancer Genome Consortium (ICGC) - India Project (IRB Project No. 3 A/c. No. 2408)

Dr. Rajiv Sarin

Duration of the Project: One year Extendable up to Three years.

Consolidated Salary: Rs. 42,000/- p.m.

Application last date: 8th January, 2015.

Interview Date & Time: 21st January, 2015, at 11.00 a.m.

Venue: Conference Room, 3rd floor, Khanolkar Shodhika, ACTREC.

Essential Qualifications and Experience:

Ph.D (any branch of Life Sciences)

The candidate must have at least one year experience after Ph.D., preferably in Genomics and Molecular Biology.

Candidates fulfilling these requirements should pre register themselves by sending their application in the prescribed format with recent CV and contact details of 2 referees by e-mail to icgc@actrec.gov.in latest 8th January, 2015 by 10.00 a.m.

Candidates shortlisted for the interview will be intimated by email on or before 9th January, 2015.

The interviews would be held on 21st January 2015 and will be only for the pre registered candidates who have been shortlisted.
No T.A./D.A. will be admissible for attending the interview.

At the time of Interview the candidate should bring original certificates along with CV with contact details of 2 referees and submit the photocopies (attested) of the certificates, with a recent passport size photograph.

Advertisement: www.actrec.gov.in/data%20files/2014/Walk-in-Research-Fellow-26-12-14.doc

gapFinisher: A reliable gap filling pipeline for SSPACE-LongRead scaffolder output

Rahul Nayak — Fri, 24 Jan 2020 06:04:40 -0600

gapFinisher is based on the controlled use of a previously published gap filling tool FGAP and works on all standard Linux/UNIX command lines. They compare the performance of gapFinisher against two other published gap filling tools PBJelly and GMcloser.

gapFinisher can fill gaps in draft genomes quickly and reliably.

Address of the bookmark: https://github.com/kammoji/gapFinisher

Comparative Genomics in Ensembl

Wed, 21 Jan 2015 08:31:11 -0600

The Ensembl browser provides viewable whole-genome alignments, homologues and phylogenetic gene trees, protein families, and ancestral sequences. Learn how to view and export these data in this video.