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

LAST can:

• Handle big sequence data, e.g:
  • Compare two vertebrate genomes
  • Align billions of DNA reads to a genome
• Indicate the reliability of each aligned column.
• Use sequence quality data properly.
• Compare DNA to proteins, with frameshifts.
• Compare PSSMs to sequences
• Calculate the likelihood of chance similarities between random sequences.
• Do split and spliced alignment.
• Train alignment parameters for unusual kinds of sequence (e.g. nanopore).

Address of the bookmark: http://last.cbrc.jp/

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.

PGIMER

Chandigarh

invites application for a project dissertation program for students who have completed their first year of M.Sc. in Bioinformatics.

This is an exciting opportunity for Master's students to train in modern methods in Bioinformatics. The duration of the training will be four to six months, starting from January 2016.

Education: Pursuing M.Sc. Bioinformatics

Essential: Post graduate applicants should have completed their first year and should be in the third semester or first half of the second year.

Only students who are willing to spend a minimum period of 4 months to a maximum of six months, without any break, would be eligible for the program.

How to Apply: Candidates interested in the above project dissertation program should apply online. Send your CV, Scanned copy of letter of recommendation from Head of Institution along with Registration form in the given format should be sent to: info@bicpgi.org

Please mention clearly “Project dissertation & your Name” in the Subject.

The last date for application is December 23, 2015

Note: Selected candidates may please note that the program is free of cost and would not provide any financial aid for transport and stay. Name of the selected candidates would be posted on the centre website by December 31, 2015.

Incomplete applications will be rejected.

For more information visit our website: http://bic-pgi.org/

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

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

Jamia Hamdard New Delhi - 110062 Additional Information States & U.T State & Union Territories Delhi How To Apply Apply Details
Last date of application: December 5, 2015 Web/Notification URL http://www.jamiahamdard.ac.in/

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

https://bioinformatics-core-shared-training.github.io/cruk-summer-school-2017/Day1/Session4-seqIntro.html

Address of the bookmark: https://bioinformatics-core-shared-training.github.io/cruk-summer-school-2017/Day1/Session4-seqIntro.html

Applications are invited in the prescribed form for filling up the following posts of Teachers and Service Personnel from the candidates who are qualified as on the last date fixed for receipt of applications in the University of Agricultural Sciences, Dharwad.

I. ASSISTANT PROFESSOR CADRE (Scale of pay Rs.15600-39100 + AGP Rs. 6000) (UGC / ICAR pay-scales)

I. Re-notified posts:

9. Assistant Professor of Bioinformatics 1 GM-1

More Info : https://sites.google.com/a/uasd.in/recruitment/

http://novelseq.sourceforge.net/Home

Paper at https://www.ncbi.nlm.nih.gov/pubmed/20385726

Address of the bookmark: http://novelseq.sourceforge.net/Home