Research Associate Biotechnology /JRF / Lab. Assistant recruitment in Indian Institute of Vegetable Research

Project:
Genomics assisted selection of Solanum chilense introgression lines for enhancing drought tolerance in tomato
Post Name : Research Associate
Qualification : Ph.D in Biotechnology/ Bioinformatics/Genetics & Plant Breeding. M. Tech in Computer Science with at least one research paper in science citation indexed journal. Desirable: Experience in bioinformatics and next generation sequence data handling. Familiarity in Linux, R, Perl/Phython or other programming languages. Willingness to travel to European partner centers.

Pay Scale : Rs. 36000 for 1st and 2nd year as per rules for Research Associate. Rs. 25000/- for 1st and 2nd year and Rs. 28000 as per rules for Junior Research Fellow. Rs. 7000/- for Lab. Assistant.

Age : Not more than 35 years for Men and 40 years for Women (Relaxable for SC/ST/OBC/PH candidates as per rules) for Research Associate/ Junior Research Fellow. Minimum age will be 21 years and maximum age will be 45 years (Relaxable for SC/ST/OBC/PH candidates as per rules) for Lab.Assistant.

More at http://iivr.org.in/Job%20Oppurtunities/RA20.03.2015.pdf

So far miniasm is in early development stage. It has only been tested on a dozen of PacBio and Oxford Nanopore (ONT) bacterial data sets. Including the mapping step, it takes about 3 minutes to assemble a bacterial genome. Under the default setting, miniasm assembles 9 out of 12 PacBio datasets and 3 out of 4 ONT datasets into a single contig. The 12 PacBio data sets are PacBio E. coli sample, ERS473430, ERS544009, ERS554120, ERS605484, ERS617393, ERS646601, ERS659581, ERS670327, ERS685285, ERS743109 and a deprecated PacBio E. coli data set. ONT data are acquired from the Loman Lab.

For a C. elegans PacBio data set (only 40X are used, not the whole dataset), miniasm finishes the assembly, including reads overlapping, in ~10 minutes with 16 CPUs. The total assembly size is 105Mb; the N50 is 1.94Mb. In comparison, the HGAP3produces a 104Mb assembly with N50 1.61Mb. This dotter plot gives a global view of the miniasm assembly (on the X axis) and the HGAP3 assembly (on Y). They are broadly comparable. Of course, the HGAP3 consensus sequences are much more accurate. In addition, on the whole data set (assembled in ~30 min), the miniasm N50 is reduced to 1.79Mb. Miniasm still needs improvements.

Miniasm confirms that at least for high-coverage bacterial genomes, it is possible to generate long contigs from raw PacBio or ONT reads without error correction. It also shows that minimap can be used as a read overlapper, even though it is probably not as sensitive as the more sophisticated overlapers such as MHAP and DALIGNER. Coupled with long-read error correctors and consensus tools, miniasm may also be useful to produce high-quality assemblies.

Minimap and miniasm are ultrafast tools for (i) mapping and (ii) assembly. Designed for long, noisy reads, they do not have a correction or consensus step, and therefore the resulting assemblies are contiguous (i.e. long) but very noisy (i.e. full of errors)

We start with an all against all comparison:

minimap -Sw5 -L100 -m0 -t8 reads.fq reads.fq | gzip -1 > reads.paf.gz

Then we can assemble

miniasm -f reads.fq reads.paf.gz > reads.gfa

Convert GFA to FASTA:

awk '/^S/{print ">"$2"\n"$3}' reads.gfa | fold > reads.fa

And then count how many contigs:

grep ">" reads.fa | wc -l

# Download sample PacBio from the PBcR website
wget -O- http://www.cbcb.umd.edu/software/PBcR/data/selfSampleData.tar.gz | tar zxf -
ln -s selfSampleData/pacbio_filtered.fastq reads.fq
# Install minimap and miniasm (requiring gcc and zlib)
git clone https://github.com/lh3/minimap && (cd minimap && make)
git clone https://github.com/lh3/miniasm && (cd miniasm && make)
# Overlap
minimap/minimap -Sw5 -L100 -m0 -t8 reads.fq reads.fq | gzip -1 > reads.paf.gz
# Layout
miniasm/miniasm -f reads.fq reads.paf.gz > reads.gfa

Address of the bookmark: https://github.com/lh3/miniasm

A walk-in-Interview is proposed to be held at National Bureau of Animal Genetic Resources, Karnal (Haryana)-132001 at 10:30 AM on 19.08.2015 to select One Research Associate & Three Senior Research Fellow as per details given below:

Name of the project & project period: ICAR Consortium Platform on Genomics.

The post duration is Upto 31.03.2017 or earlier & Co-terminus with the project.

Upto 31.03.2017 or earlier and Coterminus with the project

Essential Qualifications: PhD degree in Bioinformatics OR Master’s degree in Bioinformatics with 4 years/5 years of Bachelor’s degree having 1st division or 60% marks or equivalent overall grade point average, with at least two years of research experience as evidenced from Fellowship/Associateship

Desirable: Working experience in Next Generation Sequencing data analysis

Emolument: Research Associates may be fixed at a consolidated amount at one of the two pay levels given below depending upon the qualification & experience.

I. Research Associate – Master Degree Holders Rs. 38,000/ + HRA II. Research Associate – Doctoral Degree Holder Rs. 40,000/ + HRA

Senior Research Fellow: Two:- Bioinformatics One: - Biotechnology.

Duration of engagement: Upto 31.03.2017 or earlier and Coterminus with the project

Essential Qualifications: Master degree in any one of discipline/ Subjects- Biotechnology/Bioinformatics with 4 years/5 years of Bachelor’s degree.

Candidates having post graduate degree in above mentioned subjects with 3 years Bachelor’s degree should have NET qualification.

Desirable: The candidates should have zeal to work in R environment and NGS data analysis Emolument: Rs. 28,000/- per month + HRA as per admissibility

Age Limit: 1. 40 year for Men and 45 years for Women in case of RA on the date of Interview. 2. 35 year for Men and 40 years for Women in case of SRF on the date of Interview. (Relaxation for SC/ST/OBC and PHC as per GOI/ICAR rules) The above positions are purely temporary and will be filled in on Contractual basis. The selected candidate shall have no right/claim for regular appointment at this Institute, as the engagement is co-terminus with the Project/Scheme.

Interested candidates may attend Walk-in-Interview at 10:30 AM on 19.08.2015 alongwith original certificates and typed bio-data with one set of attested copies of each their certificates with passport size photograph. No TA/DA will be paid for attending the interview. All eligible candidates are advised to be present at least 30 minutes before scheduled time on the date of interview for completing necessary formalities. Canvassing in any form will disqualify the candidates.

More at http://210.212.93.85/Advertisiment3.pdf

https://github.com/ewijaya/slidesort-bpr

Address of the bookmark: https://code.google.com/archive/p/slidesort-bpr/

No of Post: 01
How To Apply: Walk-in interview will be held on 24-03-2015 at 10:00 AM at NRCPB, New Delhi for filling Research Associate and Senior Research Fellow positions as mentioned below. The positions are temporary and are initially offered for a period of one year. Details such as emoluments, qualifications, application format etc., are given below. Desirous candidates should report for interview latest by 10:30 AM with the application in the prescribed format, copies and originals of certificates, thesis and documents. No TA/DA will be provided for attending the interview
General Instructions: The positions are purely temporary, on a contractual basis and are initially offered for one year. The period and duration of the scheme is tentative and the same may change. The person employed will have no right to claim employment or engagement in ICAR at the end of the contract period. No TA/DA will be provided for appearing in the interview. Persons already in employment should bring “No Objection Certificate” from their present employer. The candidates must bring with them five copies of the CV in the format given below along with original documents such as t h e s i s , degree certificates, marks sheets, publications, experience certificate etc. for verification and one set of self attested copy of all certificates. The decision of the Project Director of this Institute will be final and binding in all aspects. In case of any disputes, it will be resolved within the jurisdiction of New Delhi Court only.
Detail of Interview: 24-03-2015
Age Limit: 35 Years
Contact Details: Ph: 011-25848783; Fax: 25843984

How to use TAREAN:

• Install a local instance of the pipeline using its source code available from bitbucket repository.
• Use  public Galaxy-based server at https://repeatexplorer-elixir.cerit-sc.cz/. The server is provided in frame of the Elixir CZ project and is maintained by CESNET and CERIT-SC. Simple registration is required to use this service.

Development of TAREAN was supported by ELIXIR CZ research infrastructure project (MEYS Grant No: LM2015047).

References

Novak, P., Avila Robledillo, L., Koblizkova, A., Vrbova, I., Neumann, P., Macas, J. (2017) – TAREAN: a computational tool for identification and characterization of satellite DNA from unassembled short reads. Nucleic Acids Res., doi:10.1093/nar/gkx257

Address of the bookmark: https://bitbucket.org/petrnovak/repex_tarean

NIPGR is commonly known as National Institute of Plant Genome Research. Recently, it’s great opportunity for those candidates who are interested to do job in NIPGR. National Institute of Plant Genome Research (NIPGR) had found to build a bridge between the branches of natural sciences and due this connection it is steeping on the heaps of success. Its objectives to preserve, research, production and the advancement in the trait are very clear and also being appreciated by the nation and had been contributing for the further enrichment of the institute. NIPGR had announced the recruitment to further make improvements and amendments by the young potential in their panel. The recruitment is being announced for the post is mentioned below. We are giving a complete information to applicants for find their eligibility as per desired post under NIPGR Recruitment 2015 project but if the candidates are not satisfied with this information then they can download an official advertisement of NIPGR recruitment 2015 from the link defined ahead under the head of reference.

NIPGR Recruitment 2015 for the 1 post of Research Associate: National Institute of Plant Genome Research (NIPGR) had instigated the progression of the recruitment and this process is linked thoroughly so as the 1 post of Research Associate. Applicants are associated and linked with the education to be PHD degree in the life science, biotechnology, bioinformatics or molecular biology. Applicants are associated with the dispatch of the application along with the required certificates so as on the date of 24th Feb 2015.

The recruitment notification and application @ http://www.nipgr.res.in/careers/vacancies_latest.php#

More at http://bcil.nic.in/default.htm