Job Description

• Work within a fast-paced, collaborative environment with small project teams working on a variety of tasks ranging from new product development to DNA data processing
• Collaborate with Centrillion research scientists in order to bridge the gap between the laboratory and the digital world
• Develop tools to enable research projects to cope with the enormous amounts of data produced by modern DNA sequencing experiments
• Build simulation algorithms to help guide and analyze research done in the lab
• Solve challenging engineering problems that require the development of innovative algorithms

Requirements

• Strong background in mathematics/statistics with a degree in a related field
• Strong analytical, coding, communication, and organizational skills
• Experience with algorithm development, simulations, and data analysis
• Proficiency in at least one modern programming language (like Python or Perl)
• Experience analyzing genetic and biological data sets (e.g., DNA data analysis and image analysis)
• Experience with machine learning and pattern recognition is preferred

Please submit your resume at https://www.centrillionbio.com/career/ to apply for this position.

https://www.hiv.lanl.gov/components/sequence/HIV/search/search.html

Address of the bookmark: https://www.hiv.lanl.gov/components/sequence/HIV/search/search.html

IIHR Vacancy Details:
Total No. of Posts: 14
Name of the Post:
1. Senior Research Fellow: 12 Posts
2. Project Assistant: 01 Post
3. Research Associate: 01 Post

Age Limit: Candidates age limit is 40 years for men & 45 years for women for RA post, 35 years for men & 40 years for women for SRF post, 30 years for men & 35 years for women for JRF post and 21 to 40 years for Other as on closing date of receipt of applications. Age relaxation is applicable as per rules.

Educational Qualification: Candidates should possess M.Sc (Ag) Plant Pathology or Microbiology or Biotechnology or Biochemistry or M.Tech (Ag) or Bioinformatics for SRF Posts, 10th class with experience in workshop (welding fitting) for Project Asst Post and M.Sc (Ag) Plant Pathology or M.Sc (Ag) Biotechnology or Ph.D in Plant Pathology or Agricultural Biotechnology for RA Post.

Selection Process: Candidates will be selected based on their performance in interview.

How to Apply: Eligible candidates may send their application in the prescribed format along with attested copies of relevant certificates and should mention name of PI/ Co-PI, Item No. of the Post & name of the post clearly on the application as well as on the cover to the Concerned PI/ Co-PI, Indian Institute of Horticultural Research, Hessaraghatta Lake Post, Bengaluru-560089 on or before 15-05-2015 and attend the interview along with originals, two passport size photographs on 26 & 27-05-2015 from 10:00 AM Onwards.

Important Dates:
Last Date for Receipt of Applications: 15-05-2015.
Date & Time of Interview: 26 & 27-05-2015 from 10:00 AM Onwards.
Venue: IIHR Campus.

More at http://www.iihr.ernet.in/content/srf-jrf-application-format

We have sequenced the CHM13hTERT human cell line with a number of technologies. Human genomic DNA was extracted from the cultured cell line. As the DNA is native, modified bases will be preserved. The data includes 30x PacBio HiFi, 120x coverage of Oxford Nanopore, 70x PacBio CLR, 50x 10X Genomics, as well as BioNano DLS and Arima Genomics HiC. Most raw data is available from this site, with the exception of the PacBio data which was generated by the University of Washington/PacBio and is available from NCBI SRA.

A UCSC browser is available for v2.0 (as well as legacy v1.0 and v1.1 versions). An interactive dotplot visualization of all genomic repeats is also available from resgen.io. Known issues identified in the assembly are tracked at CHM13 issues.

MORE at https://github.com/marbl/CHM13

Address of the bookmark: https://www.science.org/doi/10.1126/science.abj6987

More at http://www.binc.co.in/College/Index_New.aspx

BINC notification http://www.binc.co.in/PdfDocuments/Notification.pdf

Few dates to remember:

Starting of online submission of application: March 9, 2015
Last date for submission of application: April 30,2015
Examination consists of two parts:
Part I (Paper I) : June 7, 2015 (10 AM-12 PM)
Part II ( Paper II & III) :June 28, 2015 (9 AM-12 PM & 2 PM-4 PM)

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

Name of the College: Karpagam University, Coimbatore

Date of official publication: 15th April 2015

The newspaper wherein this job advertised: The Hindu Newspaper

Name of the posts: Senior Professors, Professors, Associate Professors and Assistant Professors

Departments:
Bioinformatics
Biotechnology
Qualifications/Eligibility: The candidates should have qualifications as M.E/M.Tech/M.A/M.Com/MBA/M.Sc/M.Phil/NET/SLET/Ph.D

Job Location: Coimbatore, TN

Salary: As per college norms

How to apply: Interested and eligible candidates are requested to apply online at http://www.karpagamuniversity.edu.in/career

Last date: As soon as possible from 15th April 2015

Reference: The Hindu Newspaper dated 15-04-2015, Coimbatore edition on 14th page

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/

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.