Project :“Genetic Transformation and Development of Elite Transgenic Maize (Zea mays L.) for Biotic and Abiotic Stresses Tolerance”.

Qualification: Ph.D. degree in:Biotechnology/Bioinformatics/Biochemistry/Plant Molecular Biology/Plant Physiology/Botany or any related area with evidence of prior experience in maize transformation.

Additional experience in plant transformation of any cereal crop would be preferable.

The appointment would initially be for one year.

How to apply
Interested applicants should send their detailed CV including brief synopsis regarding the previous research experience (along withcontact email address by email) to: Dr. Tanushri Kaul (tanushri@icgeb.res.in). Group Leader, Nutritional Improvement of Crops Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi-110 067.

Closing date for applications: 22 August 2016.

More at http://www.icgeb.org/vacancies.html

Address of the bookmark: https://github.com/soedinglab/metaeuk

Senior Manager (Bioinformatics Operations)
No. of posts: 01 (General)
Pay Scale: PB-3 15600-39100 + Grade Pay Rs.6600/-
Min. Qualification: PhD in Bioinformatics, , Life Sciences or Computer Science applied to biological questions.
A Min. 5 years of experience
Age limit: 40 years as on August 01, 2016

More at http://www.rgcb.res.in/positions.php

Please note that the CrowdGO snakemake workflow is currently only tested on Ubuntu. It should work on OSX, but please report any errors to maarten.reijnders@unil.ch or create an issue.

https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1010075

Address of the bookmark: https://gitlab.com/mreijnders/crowdgo

More at http://www.nabi.res.in/Vacancies/NABI/ResearchFellowships/JRFSRFRA/2016/NABI8(18)2012-PME-3/Advt.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

Note: Experience in the following field required: Molecular cancer cytogenetic and genetic toxicology Molecular drug Designing and targeted therapy Cancer genomics, proteomics, bioinformatics and next generation sequencing Therapeutic stem cell research and gene therapy Molecular cancer immunology and immunotherapy Molecular epidemiology Tumor endocrinology Translation research Ultra structural/tissue engg/development biology research Virus and cancer Molecular pathology No. of Posts: 11 (Eleven), (SC-1, OBC-3, UR-7)

Location: Kolkata (Calcutta) Salary: Rs.15600-39100 + Grade, Pay Rs.5400/-

For details kindly refer to the Employment News dated 24-30 September, 2016 and in the Institute’s Website: http://www.cnci.org.in

Last date for receipt of applications is 30 days from the date of notification in the Employment News. Director Chittaranjan National Cancer Institute 378, S.P.

Institute’s Website: http://www.cnci.org.in

You should begin by downloading the program from here. You will need to choose the link that matches your computing platform and then follow the instructions for opening the download package.

Once you have done this, you will be ready to try some example analyses on the test data that are provided with the download. The section on Examples shows how to use the most common IMPUTE2 functions. We suggest that you work through these examples and try to understand what the elements of each command are doing. If you don't understand something or would like to know if the program can perform a function that isn't listed, you can read our FAQ or submit a question to our mail list.

When you have learned the basic functionality of the program, you can use several features of this website to prepare your own analysis:

• Learn about best practices for imputation.
• Download reference data that you can use to impute genotypes in your study.
• Look through a complete list of program options.

Address of the bookmark: https://mathgen.stats.ox.ac.uk/impute/impute_v2.html

Research Associate :
Essential Qualification: Ph.D in Bioinformatics/Biotechnology/Life Science from a reocngised univeristy/institute
Pay: Rs.36000-/- + Admissible 10% HRA per month
Age: Below 35 years

Junior Research Fellow
Essential Qualification: M.Sc in Bioinformatics/Biotechnology/Life Science from a reocngised univeristy/institute
Pay: Rs.18000-/- + per month
Age: Below 35 years

Last date for receving application by mail or post is 08.11.2016

Company Info.
North-Eastern Hill University

Bioinformatics Infrastructure Facility (BIF) Department of RDAP North-Eastern Hill University, Tura Campus Tura-794002, Meghalaya

More at http://www.nehu.ac.in/Advertisements/BIFTuraManpowerAdvt_25102016.pdf