BOL: Related items

Quick next generation sequencing (NGS) terms definition

Neel — Fri, 09 Jun 2017 04:52:26 -0500

fragment size: the Illumina WGS protocol generates paired-end reads from both ends of longer fragments. The lengths of these fragments are assumed to be sampled from a normal distribution. Therefore, in the absence of structural variants, mapping locations of the paired ends span within an interval [δmin,δmax]. Most (>90%) of paired-end reads are sampled from no-SV regions, therefore the fragment size distribution can be learned empirically for each WGS data set separately.

concordant reads: a read pair is called concordant if they can be mapped to the reference genome as “expected”: (a) mapped to opposing strands where the upstream read is mapped to the forward strand and the downstream read is mapped to the reverse strand2, (b) the distance between ends is between the minimum and maximum expected fragment size.

discordant reads: briefly, any non-concordant read pair is considered discordant. Note that, by definition, the discordant read pairs signal potential SVs. The sequence signature produced by these type of reads is known as read-pair signature.

split reads: a read that can only be mapped to the reference genome by breaking into two sub-reads is called a split-read. These types of reads also indicate a potential SV or a short insertion or deletion (indel).

read depth: number of reads that map within a region of the genome. Overall genome-wide read depth is also referred to as depth of coverage. It is expected that the number of reads that “cover” each base-pair to follow a Poisson distribution. Therefore, if the read depth over a certain region deviates significantly from this distribution, it signals for a potential copy number variation (CNV).

Research Associate Bioinformatics Central Institute for Research on Buffaloes (CIRB) - Hisar, Haryana

Fri, 31 Jul 2015 10:19:45 -0500

Research Associate (RA) under Network Project on Agricultural Bioinformatics

Name of the Project : Network Project on Agricultural Bioinformatics Number of positions One
Qualifications : Ph.D Degree in Bioinformatics/Biotechnology/ Biochemistry/Genetics & Breeding/Life Sciences OR Master’s Degree in relevant subject with at least 2 years research experience. Desirable : Working experience in Molecular Biology/Genomics/Bioinformatics, specifically, sequence data analysis using software’s proficiently

Emoluments : Masters Degree Holders Rs. 38,000/- per month Doctoral Degree Holders Rs. 40,000/- per month

Emoluments : Rs.25000/- per month for 1st and 2nd year and Rs. 28000/- per month for 3rd year
Age Limit : Upper age limit is 35 years for men and 40 years for women on the date of interview. Age relaxation for SC/ST and OBC candidates as per rules

More at http://www.cirb.res.in/attachments/195_walk-in-interview%20for%20contractual%20positions%20of%20RA%20and%20SRF%20%28On%20Dated%2011.8.2015%29.pdf

RA Bioinformatics at TEZPUR UNIVERSITY

Fri, 06 Feb 2015 04:11:23 -0600

Walk-in-interview will be held on 23 February, 2015 at 11.00 a.m. for the following temporary positions in the DBT (U-EXCEL) sponsored project entitled “Sequencing genomes of some bacteria that invade/resides in tomato plant” under the Principal Investigator Dr. Suvendra Kumar Ray, Department of Molecular Biology and Biotechnology, Tezpur University.

Interested candidates may appear before the interview board on 23 February, 2015 at the Office of the Head, Department of Molecular Biology & Biotechnology, Tezpur University with original documents and photocopies of marks sheets, certificates, testimonials, caste certificate (if applicable), experience certificate and a copy of curriculum vitae (CV) duly signed by the candidate.

Position: One (01) Research Associate.

Educational Qualification: Candidates having Ph.D. degree or submitted thesis in any topic of Life Science Areas (Zoology, Botany, Microbiology, Biotechnology etc.) along with knowledge of gene and protein sequence analysis may apply.

Remuneration: Rs. 22,000/- (Rupees twenty two thousand) only + 10% HRA as admissible per month for the first year and Rs. 23,000/- (Rupees twenty three thousand) only + 10% HRA as admissible per month for the second year.

Age: Candidate preferably below the age of 40 years who have obtained a doctorate (Ph.D.) degree from a recognized University.

Upper age limit may be relaxed up to 5 years in the case of candidates belonging SC/ST/OBC/Women and physically challenged.

Position: One (01) Project Assistant.

Educational Qualification: B.Sc./B.Tech./B.E./B.Pharma in any branch with minimum 55% mark in the qualifying examinations and minimum 50 % mark in 10th and 10+2 Science examinations.

Remuneration: Rs. 8,000/- (Rupees eight thousand) only per month (consolidated). Age: Candidate should not be more than 28 years of age on the date of interview. Upper age limit may be relaxed up to 5 years in the case of candidate belonging to SC/ST/OBC/Women/Physically Challenged.

Duration: One year or till completion of the project, whichever is earlier. N.B. No TA/DA will be paid to the candidates for attending the interview.

For further information contact – Dr. Suvendra Kumar Ray, Associate Professor Email: suven@tezu.ernet.in Department of Molecular Biology and Biotechnology Tezpur University Sd/- Dean, Research & Development Tezpur University

Advertisement: http://www.tezu.ernet.in/ProjectWalkin/Advt-SKR2-5342-A.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

RA WALK-IN-INTERVIEW @ ACTREC

Mon, 09 Feb 2015 01:06:16 -0600

No. ACTREC/Advt./ 7 /2015

Title of the Project
Research Associate
(One position)
DBTs Biotechnology/Bioinformatics training centre
PI Dr. Ashok Varma

Duration of the Project Six Months from the date of appointment, can be extended further for six month.

Date & Time: 17th February, 2015 at 10.00 a.m.

Venue: Meeting Room, 3rd floor, Khanolkar Shodhika, ACTREC

Essential Qualifications and Experience:

Ph.D. Degree in Basic Sciences from recognized University. Research experience in Bioinformatics or on gene cloning, protein purification, and crystallization.

*M.Sc. degree obtained after a one year course will not be considered.

Selected candidate will have to join at the earliest.

Consolidated Salary: Rs.28,600/- p.m. {Rs.22,000/- + 30% HRA}

The work progress of the candidate will be monitored and extension after 6 months will depend on satisfactory progress of the work.

Candidates fulfilling these requirements should pre-register by sending their application in the prescribed format with recent CV and contact details of 2 referees by e-mail to ‘program.office@actrec.gov.in’ latest by 17.00 hrs on 12-02-2015.
The interviews would be held on 17th February, 2015 and will be only for the pre-registered candidates. Candidates should report between 09.30 to 10.00 a.m. in Steno Pool, 3rd floor, Khanolkar Shodhika, ACTREC, Kharghar, Navi Mumbai.
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.

All correspondence should be strictly made only to ‘program.office@actrec.gov.in’ as indicated.

Advertisement: www.actrec.gov.in/data%20files/2015/AV-RA-DBT-28-1-15.docx

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

Summer Intern - Research Bioinformatics

Mon, 16 Feb 2015 12:26:32 -0600

Be proficient in LINUX, know perl or python, understand biology and Next Generation Sequencing.
The intern will port Agile Assay Design pipelines into Galaxy.
The intern will also learn to develope his/her own bioinformatics pipelines for PCR or NGS data analysis.

Who you are
You’re someone who wants to influence your own development. You’re looking for a company where you have the opportunity to pursue your interests across functions and geographies. Where a job title is not considered the final definition of who you are, but the starting point.

Qualifications:
Major: Bioinformatcis or biology major who is interested and wants to learn Biocomputing, At least 2 years of college.
Basic knowledge of LINUX and programming, e.g., perl, python, XML.

More at http://www.roche.com/careers/jobs/jobsearch/job.htm?id=E-00437679&locale=en&title=Summer%20Intern%20-%20Research%20Bioinformatics

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

JRF Bioinformatics @ IISR, Kozhikode

Tue, 24 Feb 2015 08:44:17 -0600

JRF Bioinformatics Jobs recruitment in Indian Institute of Spices Research on temporary basis

Name of the Scheme : Distributed Information Sub Centre – DISC

Qualifications : M.Sc/ B Tech in Bioinformatics with NET/GATE or M Tech in Bioinformatics

Number of posts : One

Emoluments : Rs. 25,000/-

Upper age limit : 35 years for Men & 40 years for Women as on date of Interview
How to apply

Date of Interview : 12-03-2015 at 10.00 AM. All relevant certificates (in original) and bio data, No objection certificate in case he/she is employed elsewhere and experience certificate in original (if any) need to be produced at the time of interview.

More at http://spices.res.in/index.php?option=com_content&view=article&id=263

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