Applications with complete bio-data from candidates possessing the required qualifications are invited for the posts of JRF (1) and Project Assistant (1) in DBT, GOI-funded research project “Next Generation Sequencing (NGS)- based de novo assembly of expressed transcripts and genome information of Orchids in North-East India” in DBT’s Twinning programme for NE as per DBT sanction order and norms.

(i) JRF(1 no.):

Qualifications: M.Tech/M.Sc in Life Sciences/ Botany/ Zoology/ Biochemistry/ Biotechnology/ Bioinformatics;

Desirable: Aptitude for Bioinformatics and Computer Programming/ Next generation sequencing data analysis

(ii) Project Assistant (1 no.):

Qualifications: Graduation in Science,

Desirable: Experience of working in a Life Science/Plant Biotechnology lab. and familiarity with computers and field work viz. collection of samples.

The applications through email bicnehu@gmail.com or post must reach the undersigned within 15 days from the date of publication of this advertisement. The advertised posts are purely temporary for the duration of the project and subject to availability of the funds from DBT. The appointment does not confer any entitlement or right over the posts for absorption in the University service. Prof. Pramod Tandon, PI/Mr. Devendra Kumar Biswal (Co-PI) email: bicnehu@gmail.com

Advertisement: www.nehu.ac.in/Advertisements/BIC_AdvtPV_030815.pdf

Parliament2 runs a combination of tools to generate structural variant calls on whole-genome sequencing data. It can run the following callers: Breakdancer, Breakseq2, CNVnator, Delly2, Manta, and Lumpy. Because of synergies in how the programs use computational resources, these are all run in parallel. Parliament2 will produce the outputs of each of the tools for subsequent investigation.

Address of the bookmark: https://github.com/dnanexus/parliament2

Jawaharlal Nehru University has been granted funds by the Department of Biotechnology (DBT), Govt. of India to initiate an Inter-School programme in JNU to strengthen training and research called "DBT-Jawaharlal Nehru University, New Delhi-Interdisciplinary Life Science Programme for Advanced Research and education" with the broad project area entitled "From Molecules to Systems: Exploring biological space using chemical and synthetic biology" cutting across Physical, Chemical and Biological Sciences.

Applications are invited for the following purely temporary posts at various levels in the various Group projects for Research and Technical positions. The project is upto March 2017, but the appointments shall be initially for a period of one year, renewable every year depending on the performance of project staff:

Project Sub-Title: Synthetic Genomics: Making sense out of 'junk' DNA

Senior Research Fellow (SRF) - 01 Post

Qualifications: M.Sc in Bioinformatics, with minimum 2 year research experience, specialization in microRNA, molecular modelling, systems and/or Synthetic biology with publication in the relevant area would be desirable.

Investigator: Prof. Pawan Kumar Dhar

Fellowship: Rs. 14000+30% HRA p.m.

Project Sub-Title: "Structure, function, and dynamics of biomolecules and Molecular engineering"

Postdoctoral Fellow (PDF) - 01 Post

Essential Qualifications: PhD in Science(Bioinformatics/Computational Biology, Physics, Chemistry, Mathematics, & Statistics), specialized in the area of Computational Biology/Structural Bioinformatics/ Quantum Chemistry/Molecular Dynamics & Simulation /Systems Biology , reflected by thesis topics and or publication of papers during PhD and/or Post doctoral experience.

Desirable Qualifications: Computational methods and designing experience in the field of Structure based or ligand based drug design, Chemoinformatics, Programming capabilities as required for developing tools in the computational & systems Biology.

Investigator: Prof. Indira Ghosh, SCIS

Salary: Rs. 22, 000 + 30% HRA

(Note: Revised emoluments shall be payable if Educational Qualifications or Eligibility Criteria as per DST OM No. A.20020/11/97-IFD dated 31-03-2010 are met by the research personnel)

The applications on plain paper indicating name, date of birth/age, address, essential / technical / professional qualifications, experience, research work, should reach the Programme Coordinator on or before 27th August 2015 at the following address:

The Envelop should be marked for the Post applied for. Any clarifications regarding projects may be sought from the respective project investigators as mentioned.

Address for correspondence:
Programme Coordinator
DBT-JNU BUILDER programme
School of Biotechnology
Jawaharlal Nehru University
New Delhi 110067

More at http://www.jnu.ac.in/career/currentjobs.htm

Project Scientist-I
Experimental / Computation analysis experience in highthroughput genomics/ clinical application.

Project Manager
Experience in handling large biological projects involving high-throughput genomics/ clinical application.

Scientific Administrative Assistant
Lab Work.

More at https://vinodscaria.genomes.in/positionsopen

The position is open for immediate appointment and available for two years and then extendable for additional one year. The applicant will be appointed as Research Associate based on qualifications as detailed below:

Research Associate:

-Master’s degree with bioinformatics with at least 2 years of research experience in Next Generation sequencing data analysis as evidence from Fellowship/ Associateship / Training / other engagements.

-Familiarity with bioinformatics tools, database development, programming skills

-Minimum 1 publication in any peer reviewed journal

Salary will be as per ICAR rules and guidelines. Application will be shortlisted based on CV, reference letters from mentors and telephonic interview. Candidates will be called for a personal interview at Bangalore before appointment. No travel expense will be provided for attending interview at Bangalore.

Interested candidates may send a Letter of Interest and CV by email to: keshav@ibioinformatics.org before September 29, 2015.

The "Ifs" of NGS QC and Trimming

1. Ensures Data Integrity
   If you want to minimize errors in downstream analyses, QC and trimming remove low-quality reads and bases, ensuring high-confidence data. This step is essential for reliable variant calling, assembly, and other applications.

2. Removes Contaminants
   If adapter sequences or contaminants are present in the raw reads, trimming can eliminate them. This prevents issues like misalignment or incorrect biological interpretations, ensuring cleaner data for analysis.

3. Improves Mapping and Assembly
   If your goal is better alignment to a reference genome or improved de novo assembly, trimming low-quality bases and adapters is critical. High-quality reads map more efficiently and generate more accurate assemblies.

4. Reduces Computational Load
   If you want to save computational resources, trimming reduces the dataset size, which speeds up processing and analysis. Clean datasets mean less computational time spent on processing low-quality data.

5. Prepares for Standardized Analyses
   If your project involves multiple datasets, QC and trimming ensure uniformity across them. This standardization makes comparisons valid and reproducible, particularly in large collaborative studies.

The "Buts" of NGS QC and Trimming

1. Risk of Over-Trimming
   But excessive trimming can lead to the loss of informative sequences, reducing read depth and potentially discarding biologically relevant data. This is especially critical in studies with limited sequencing depth.

2. Bias Introduction
   But trimming algorithms might introduce biases, especially if they inadvertently remove sequences with specific biological patterns. This can skew results and compromise biological insights.

3. Loss of Context in Paired-End Reads
   But trimming one read in a pair more than the other can lead to loss of pairing information. This complicates downstream analyses that rely on paired-end data, such as structural variant detection.

4. Time and Resource Intensive
   But running QC and trimming for large datasets can be computationally expensive and time-consuming. As sequencing depth increases, preprocessing becomes a bottleneck in the analysis pipeline.

5. Variable Standards
   But the criteria for trimming (e.g., quality threshold, minimum read length) can vary between tools and datasets. This variability may affect reproducibility and comparability of results across studies.

Balancing the "Ifs" and "Buts"

To maximize the benefits of QC and trimming while mitigating the challenges, consider the following best practices:

• Use QC Tools Wisely: Start with tools like FastQC to identify quality issues in your raw data. Visualizing quality metrics helps tailor your trimming parameters.

• Choose Reliable Trimming Tools: Tools like Trimmomatic, Cutadapt, and BBduk offer adaptive and customizable trimming options. Select one that aligns with your dataset and project goals.

• Set Reasonable Parameters: Avoid over-trimming by setting quality thresholds and minimum read lengths that balance data retention and quality improvement.

• Test Downstream Effects: Validate the impact of QC and trimming on downstream analyses, such as alignment efficiency, variant calling accuracy, or assembly quality.

• Document Your Workflow: Maintain detailed records of the parameters and tools used for QC and trimming. This ensures reproducibility and enables better troubleshooting.

Conclusion

NGS quality control and trimming are essential steps to ensure reliable and accurate data for analysis. While the "ifs" highlight the clear benefits of these steps, the "buts" remind us of the potential pitfalls. By adopting best practices and carefully balancing these considerations, you can optimize your preprocessing workflow and unlock the full potential of your sequencing data.

Working with other members of the TNDRG you will analyse complex genomic and epidemiological datasets, evaluating which computational tools are most suitable. You will contribute to the generation of innovative tools for linking epidemiological and multilevel omics datasets, ensuring that computer programs are written in a form that other collaborators can use and expand.

You will have or be close to completion of a PhD in either: bioinformatics; neuroscience; machine learning; statistics; epidemiology; neurology; or other relevant field. You will have experience programming on either R, Matlab, Python, C++, Java or any other imperative, object oriented or functional language.

Please direct Informal enquiries to Dr Alejo Nevado-Holgado (alejo.nevado-holgado@psych.ox.ac.uk).

You will be required to upload a supporting statement explaining how you meet the selection criteria for the post, a CV, and details of two referees as part of your online application.

The closing date for applications is 12.00 midday on 2 September 2015. Interviews will be held on Tuesday 15 September 2015.

https://www.recruit.ox.ac.uk/pls/hrisliverecruit/erq_jobspec_version_4.jobspec?p_id=118696

• Whole-genome sequencing
• Whole-exome sequencing
• RNA-seq (speical mode available)
• ChIP-seq

Address of the bookmark: http://qualimap.bioinfo.cipf.es/

Junagadh Agricultural University has given a recruitment notification to fill the posts of Senior, Junior Research Fellows in the establishment.

Name & No: of Posts:

1. Senior Research Fellow: 05
2. Junior Research Fellow: 05

Title of the Projects under Senior Research Fellow:

1. Molecular mapping of important traits and their transfer through marker assisted selection in Groundnut and cotton
2. Aflatoxin and its management in groundnut at Saurashtra region of Gujarat.
3. Improvement in Agricultural Production through nanotechnological inventions at Junagadh.
4. Synthesis and Characterisation of chitosan based NPK-Nano fertilizers

Title of the Projects under Junior Research Fellow:

1. Improvement in Agricultural Production Through Nanotechnological Inventions at Junagadh.
2. Synthesis and Characterisation of chitosan based NPK-Nano fertilizers

Required Eligibility Criteria:

1. Senior Research Fellow:

Age Limit: Candidates age must be maximum 35 years
Educational Qualification: M.Sc in Nanotechnology/Biotechnology/Bioinformatics
Salary: Rs. 16,000/- + HRA for first and second year, Rs. 18,000/- + HRA during third year

2. Junior Research Fellow:

Age Limit: Candidates age must be maximum 30 years
Educational Qualification: B.Sc or M.Sc degree in the field of Nanotechnology/Biotechnology
Salary: Rs. 9,600/- , Rs. 14,400/- p.m

Eligible candidates may attend the walk-in-interview on 10-09-2015 with necessary certificates of testimonials

Click Here for Detailed Recruitment Notification
http://www.jau.in/attachments/Advt/BiotechSRFJRF.pdf

Address of the bookmark: https://github.com/fenderglass/Flye