The duly completed application on prescribed format along with copies of supporting documents must reach to: Office of the Dean (Research & Consultancy), Motilal Nehru National Institute of Technology, Allahabad-211004 on or before 03/07/2015.

The position is purely temporary and will be governed by the funding agency rules & service conditions of Office of the Dean (Research & Consultancy), MNNIT Allahabad.

For detail advertisement see: www.mnnit.ac.in/images/newstories/Advertisement_for_the_post_of_Research_Assistant_in_UPCST_Project_of_Biotechnology_Department.pdf

Address of the bookmark: https://github.com/legumeinfo/gcv

Features

• Circular and linear views of genomes

• Capable of drawing genomes up to 10 Mbp with 1000's of features and 100's contigs

• Smooth zooming down to the sequence level

• Easily generate features and plots directly form the sequence (e.g. ORFs, GC-content and GC-Skew)

• Save high resolution PNG maps up to 8000x8000px

• Fully documented API for interacting with CGView.js maps

Address of the bookmark: https://js.cgview.ca/

Eligibility : M Phil / Phd, MSc

Location : Delhi

Last Date : 27 Jun 2015

Hiring Process : Walk - In
Indian Agricultural Statistics Research Institute (IASRI) - Job DetailsDate of posting:03 Jun 15

Research Associate Statisticsjob position in Indian Agricultural Statistics Research Institute (IASRI)
on purely contractual temporary basis

Project : “ICAR-Network Project of Transgenic in Crops”

Qualification : Ph.D. in Bioinformatics/ Agricultural Statistics/ Statistics/ Computer Science/ Computer Application/ Life Science/ Biotechnology/ Agricultural Science or equivalent OR Post-Graduation in Bioinformatics/ Agricultural Statistics/ Statistics/ Computer Science/ Computer Application/ Life Science/ Biotechnology/ Agricultural Science or equivalent with 1st Division or 60% marks or equivalent with at least two years of research experience.

No.of Post: 01

Emoluments for RA: Consolidated Rs. 24000/- per month + 30% HRA for Ph.D holders and consolidated Rs. 23000/- per month + 30% HRA for Master Degree.

Age Limit : 40 years
How to apply

Walk-in-interview will be held on 27th June 2015, 10.30 A.M at IASRI, Pusa, New Delhi

More at http://iasri.res.in/employment/employment.htm

What is Genome Assembly?

Genome assembly involves piecing together short DNA sequence reads generated by sequencing platforms (e.g., Illumina, PacBio, Oxford Nanopore) into longer, contiguous sequences called contigs. This can be performed as:

• De Novo Assembly: Without a reference genome.
• Reference-Guided Assembly: Using a reference genome to guide the assembly process.

Step 1: Preparing Your Data

Before starting the assembly, ensure that your raw sequencing data is high quality.

1. Input Data

   • Short Reads: Illumina sequencing generates short, accurate reads ideal for scaffolding.
   • Long Reads: PacBio and Nanopore sequencing provide long reads for resolving repetitive regions.

2. Quality Control (QC)
   Use tools like FastQC or MultiQC to assess the quality of your reads:

   fastqc reads.fastq multiqc .

   Look for issues like low-quality bases, adapter contamination, or overrepresented sequences.

3. Read Trimming and Filtering
   Trim low-quality bases and adapters using Trimmomatic or Cutadapt:

   trimmomatic PE reads_R1.fastq reads_R2.fastq trimmed_R1.fastq trimmed_R2.fastq \ ILLUMINACLIP:adapters.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:36

Step 2: Choosing an Assembly Strategy

Select an assembly strategy based on your data type:

• Short-Read Assemblers:

  • SPAdes: Popular for microbial genomes.
  • Velvet: Fast for smaller genomes.

• Long-Read Assemblers:

  • Canu: Ideal for long-read datasets.
  • Flye: Versatile for small and large genomes.

• Hybrid Assemblers:

  • MaSuRCA: Combines short and long reads.
  • Unicycler: Optimized for bacterial genomes.

Step 3: Running the Assembly

3.1. SPAdes (Short-Read Assembly)

SPAdes is an excellent choice for small genomes, such as bacteria.

The output includes assembled contigs (contigs.fasta) and scaffolds (scaffolds.fasta).

3.2. Canu (Long-Read Assembly)

Canu is designed for high-error long reads from PacBio or Nanopore.

The output will be in canu_output/genome.contigs.fasta.

3.3. Hybrid Assembly with Unicycler

Unicycler combines short and long reads for improved assemblies.

Step 4: Assessing Assembly Quality

After assembly, evaluate its quality using the following tools:

1. QUAST
   QUAST generates assembly statistics, such as N50, genome size, and GC content:

   quast contigs.fasta -o quast_output

2. BUSCO
   BUSCO checks genome completeness by identifying conserved genes:

   busco -i contigs.fasta -o busco_output -l fungi_odb10 -m genome

3. Assembly Graph Visualization
   Visualize assembly graphs with Bandage:

   Bandage load assembly_graph.gfa

Step 5: Post-Assembly Steps

1. Polishing
   Improve assembly accuracy using tools like Pilon (for short reads) or Racon (for long reads).

   racon long_reads.fasta mapped_reads.sam contigs.fasta > polished_contigs.fasta

2. Scaffolding
   Link contigs into scaffolds using tools like SSPACE or Opera-LG if required.

3. Annotation
   Annotate the assembled genome using Prokka for prokaryotes or Maker for eukaryotes.

   prokka --outdir annotation_output --prefix genome contigs.fasta

Step 6: Sharing and Archiving

1. Submit to Public Repositories
   Share your assembly in databases like NCBI GenBank, ENA, or DDBJ.

2. Metadata Preparation
   Include detailed metadata for your submission, such as organism name, sequencing platform, and coverage.

Best Practices

• Always perform quality checks at each stage to ensure data integrity.
• Use multiple tools to cross-validate results when working with complex genomes.
• Document parameters and software versions for reproducibility.

Conclusion

Genome assembly is a powerful process that transforms raw sequencing data into a coherent representation of an organism’s genome. By following this step-by-step guide, you can successfully assemble genomes and uncover valuable biological insights. Whether you’re assembling a microbial genome or tackling the complexities of a eukaryotic genome, these tools and strategies will set you on the path to success.

Starting 15th July 2015, the position relates to a project specifically for in silico drug docking, screening, design, optimisation and linkage with active chemists.

Experience in many docking softwares and operating systems is essential.

Additional experience in bioinformatics and computational biology tools will be useful.

Submit curriculum vitae to: sb.icgeb@gmail.com

Closing date: 5 July 2015

The new features include

(i) building gene-based and supermatrix-based phylogenies using a single command,

(ii) testing and visualizing evolutionary models,

(iii) calculating distances between trees of different size or including duplications, and

(iv) providing seamless integration with the NCBI taxonomy database.

ETE is freely available at http://etetoolkit.org

Address of the bookmark: http://etetoolkit.org

Job Description

The Global Trait Discovery Informatics (GTDI) group located at the DuPont Knowledge Centre (DKC), Hyderabad, India is currently seeking applications for a highly motivated computational biologist. The GTDI group contributes to research programs in plant biotechnology at the DKC as well as across research centers located in DuPont Pioneer, Johnston, Iowa and at the DuPont Experimental Station in Wilmington, Delaware.

We are looking for candidates who have experience in analysis of high-throughput -omics datasets. The researcher will be primarily responsible for analyzing diverse -omics datatypes, such as transcriptomics, proteomics and metabolomics and actively contribute towards building streamlined solutions.

The candidate will be part of a diverse team of experimental biologists, computational biologists and software developers. A critical aspect of this position involves working with global teams across multiple locations and will require effective project coordination and communication skills. This is an exciting opportunity for candidates with strong data driven skills, who want to work at the interface of computational and experimental biology and contribute towards scientific discovery.

Responsibilities

·Integrate and analyze multiple datatypes in the context of experimental observations with a goal towards formulating testable hypothesis.

·Understanding the research questions from experimental biologists and formulate relevant in silico analyses.

·Establish and implement systematic analysis workflows starting from processing of raw data to biological interpretation.

·Critically analyze a wide variety of experimental data with a view to solving the underlying research questions.

·Identify and generate datasets for scientific testing and evaluation of algorithms.

Qualifications

PhD in computational biology, bioinformatics, population genetics, complex systems, computer sciences or any relevant physical or mathematical sciences, with experience in analyzing diverse -omics datasets.

Job Qualifications

Qualifications

PhD in computational biology, bioinformatics, population genetics, complex systems, computer sciences or any relevant physical or mathematical sciences, with experience in analyzing diverse -omics datasets.

More at http://careers.dupont.com/jobsearch/job-details/research-scientist/006077W-01/

Adv. No. URDIP/ 15/2015

Opportunity for young Bioinformatics Professionals to make a career in the area of Intellectual Property

CSIR has set up a Unit for Research and Development of Information Products (CSIRURDIP) at Pune to work in the area of scientific informatics. One of the major focus areas of research work at CSIR-URDIP is PATENT INFORMATICS. With the increasing applications of Bioinformatics in the areas of life sciences industry such as Agriculture and Health Care (Diagnostics and Drugs), the output of research in these area is being protected by different forms of Intellectual Property rights. Realizing the importance of IP in the Bioinformatics field, Department of Biotechnology (DBT) has sanctioned a project on “Development, Facilitation and Harvesting of Bioinformatics related Intellectual Property” at CSIR-URDIP.

The project will involve application of Patent Informatics tools and techniques to Bioinformatics (including creation of patent landscapes, preparation of techno-legal reports of patentability, freedom to operate studies) to help protect IPRs and develop and conduct training programmes on IPRs related to Bioinformatics.

CSIR-URDIP invites applications from young Bioinformatics professionals to work on this emerging area which offers challenging opportunities and attractive career possibilities in future.

Position I: Research Associate

No of Positions: One

Consolidated amount Payable: = Rs 26,400.00

Qualification: PhD in Bioinformatics. In exceptional cases, candidature of M. Tech. candidates with First class in Bioinformatics with three years of relevant work experience will also be considered.

Job requirement: The prospective candidate will be expected to identify patents/scientific literature in field of Bioinformatics, evaluate them Vis a Vis other patents in fields and come up landscape / FTO / Patentability reports.

Age Limit: 35 years.

The candidates meeting the above criteria may appear for walk in interview at their cost on Monday 13th July 2015 at 02:00 p.m. with the CV and supporting documents (original plus copies) at the following address: CSIR Unit or Research and Development of Information Products (URDIP), "Tapovan" S.No. 113 & 114, Near NCL Colony Baner Side Gate, NCL Estate, Pashan Road, Pune-411008, Maharashtra, India

Advertisement: www.urdip.res.in/download/DBT_RA_Advt_July%202015.pdf