Address of the bookmark: https://github.com/sc932/ALE

To find repeats in a genome from 2 to 9 length using a Perl script, you can use the RepeatMasker tool with the "--length" option[0]. Here's a step-by-step guide:

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.

Key Findings:

1. Chromosomal Fusion and Its Molecular Signature:

   • The fusion site is located at 2q13–2q14.1 and is characterized by degenerate telomeric sequences appearing interstitially, indicating the historical head-to-head joining of ancestral chromosomes.
   • Despite being a signature of a past fusion event, these telomeric repeats are no longer functional and have undergone sequence degradation over time.

2. Extensive Duplications in the Surrounding Genomic Region:

   • The study identifies large-scale segmental duplications flanking the fusion site, with several of these regions duplicated and scattered across multiple chromosomes.
   • These duplications are predominantly located in subtelomeric and pericentromeric regions, suggesting their role in genomic instability and chromosomal evolution.

3. Paralogous Regions and Their Evolutionary Relationships:

   • A 168-kilobase (kb) segment near the fusion site has 98%–99% sequence identity with three regions on chromosome 9 (9pter, 9p11.2, and 9q13).
   • Another 67-kb region distal to the fusion site shows a high degree of homology to sequences in chromosome 22qter.
   • Additionally, a 100-kb segment exhibits 96% sequence identity with a region in chromosome 2q11.2.

4. Comparative Genomics and Evolutionary Implications:

   • By comparing the duplicated sequences and their arrangement in primates, the researchers traced the order of duplication events leading to their present distribution.
   • The presence of specific repetitive elements within these duplicated segments serves as evolutionary markers that help infer their historical rearrangements.
   • Some of these duplicated regions are associated with chromosomal inversion breakpoints, potentially contributing to evolutionary changes in primates.
   • Recurrent structural rearrangements in these regions have been linked to human chromosomal disorders.

Conclusions and Implications:

• The findings provide valuable insights into the structural evolution of human chromosome 2, which played a crucial role in human speciation.
• Understanding these segmental duplications and their evolutionary trajectories sheds light on genomic instability, which may contribute to human genetic diseases.
• The study highlights how large-scale chromosomal rearrangements, such as fusion and duplication, have influenced the evolutionary divergence of humans from other primates.

This research advances our understanding of human genome evolution and offers a foundation for studying the effects of structural variants in genetic disorders.

Bachelor/ BS Bioinformatics at
1. Al-khair University, Bhimber
2. Government College University, Faisalabad
3. University Of Agriculture, Faisalabad
4. Comsats Institute Of Information Technology [isb], Islamabad
5. International Islamic University, Islamabad
6. Quaid-e-azam University, Islamabad
7. Khushal Khan Khattak University, Karak
8. Virtual University Of Pakistan, Lahore
9. Virtual University Of Pakistan, Lahore
10. Hazara University, Mansehra
11. Shaheed Benazir Bhutto Women University, Peshawar
12. Comsats Institute Of Information Technology, Sahiwal
13. Capital University Of Science And Technology, Islamabad
14. Foundation University, Islamabad
15. Baqai Medical University/hospital, Karachi
16. Institute Of Business And Technology(main Campus), Karachi
17. Sir Syed University Of Engineering & Technology, Karachi
18. Forman Christian College, Lahore
19. Qarshi University (lhr), Lahore
20. The Superior University, Lahore
21. University Of Management And Technology, Lahore
22. Federal Institute Of Health Sciences, Lahore
23. Shaheed Benazir Bhutto Women University Peshawar, Sub Campus, Swabi
24. Government Postgraduate College ( Mandian), Abbottabad
25. Federal Institute Of Health Sciences, Multan
26. Fedral Institute Of Health Sciences, Muzaffarabad
27. The Limit Institution Of Health Sciences, Sahiwal

Master/ MS Bioinformatics cources at
1. Government College University, Faisalabad
2. Comsats Institute Of Information Technology [isb], Islamabad
3. International Islamic University, Islamabad
4. National University Of Science & Technology, Islamabad
5. Quaid-e-azam University, Islamabad
6. University Of Sindh, Jamshoro
7. Virtual University Of Pakistan, Lahore
8. Hazara University, Mansehra
9. Shaheed Benazir Bhutto Women University, Peshawar
10. Capital University Of Science And Technology, Islamabad
11. Cecos University Of Information Tech. & Emerging Sciences, Peshawar

The real bioinformatics scope lies if there are research labs which work in this field. One has to take account of that. If so then try to get information of those labs and visit them to get a hang of the work they pursue.

There is a huge buzz of precision medicine in light of genomics all around the world. One should also try to see how genomics infrastructure is built up or standing in Pakistan. If research labs having collaboration with hospitals employ genomics then one must also visit such labs. This will bring new avenues in healthcare advances. Not only it opens up the wealth of knowledge one can make out of genomics study but will also advance the critical thinking of therapies.

So I would encourage to target research labs working in the fields and also get information of hospitals employing genomics, this will give you an overall understanding of the fields demand in your country.

Bii.a-star.edu.sg

Bio research and development. Has course information and research information.

Isb-sib.ch

SIB operates the ExPASy proteomics server and the Swiss node of EMBnet. Teaching activities include a series of post-graduate courses given at the Universities of Geneva and Lausanne, as well as at the EPFL, and a Masters Degree in bioinformatics. Major research areas include the development of integrated databases and software resources in the field of proteomics.

Bioinformatics.ca

Provides information about bioinformatics in Canada. Workshops, certification and resources.

Chickscope.beckman.uiuc.edu

Students raise chicken embryos in the classroom and obtain magnetic resonance images through the Internet.

Bcb.iastate.edu

Graduate program at Iowa State University offering Undergraduate Major (BCBio) and the PhD program (BCB).

Bu.edu/bioinformatics/

Interdisciplinary PhD and Masters Programs that include an internship in the local industry companies. In conjunction with the NE masters program.

Bioinformatics.ubc.ca

A computational biology research centre covering many areas of genomics, proteomics, computer science and statistics. Research, training, news and events, resources and support, director's message, faculty and personnel.

Openhelix.com

Provides onsite training on specific bioinformatics databases and tools. Also offers bioinformatic software testing and research consulting services.

Igb.uci.edu

Specializing in making publicly available software and database services for computational biology.

Bioinformatics.pe.kr

Maintained by Dr. Seyeon Weon, Korea providing information on courses, a database archive, software archive and online resources.

Groups.yahoo.com/group/bimatics/

Bioinformatics group for students interested and/or working in the bioinformatics/computationalbiology fields. Offers opportunities to exchanging information and sharing ideas.

Ncbi.nlm.nih.gov/books/NBK22183/

Information about several medically important genes and related diseases. Illustrates the use of bioinformatics in their study.

Bioinfo.mbb.yale.edu/mbb452a/2003/

Bioinformatics course at Yale University. All course slides are available online.

Cs.iastate.edu/~honavar/comp-bio-courses.html

Listing of computational molecular biology course pages that have extensive online course materials.

Bioinf.manchester.ac.uk/dbbrowser/bioactivity/prefacefrm.html

A web-based tutorial associated with "Introduction to bioinformatics" published by Addison Wesley Longman.

Northeastern.edu/bioinformatics/

From the Biology department and in cooperation with Boston University. Emphasis on the ability to integrate knowledge from biological, computational, and mathematical disciplines.

Biocomp.unibo.it/lsbioinfo/

A two year, international master's programme in bioinformatics at the Universita di Bologna, Italy.

Cs.helsinki.fi/bioinformatiikka/mbi/programme.html

A two year Masters Degree Programme in Bioinformatics (MBI) offered by the University of Helsinki and Helsinki University of Technology, Finland.

Ornl.gov/sci/techresources/Human_Genome/education/education.shtml

A resource for introductory information on the Human Genome Project.

His.se/bioinformatics

A one-year, international master's programme in bioinformatics at the University of Skovde, Sweden.

Members.tripod.com/C.elegans/

Resources in biochemical, molecular, cellular, system, and organism biology, including over 25,000 indexed links, accumulated since 2000, from topic menus or from search interface.

Bioinformatics.org/faq/#contents

Summary of basics of bioinformatics for the intelligent newcomer.

Jiscmail.ac.uk/archives/bioinformatics.html

Forum featuring various aspects, events and developments in the bioinformatics field.

Biinoida.blogspot.com

Blog focusing on bioinformatics, biotechnology, pharma regulatory affairs, IPR and clinical trials.

Colorbasepair.com/bioinformatics_courses_tutorials.html

A list of on-line course materials and tutorials for bioinformatics and computational biology.

Geospiza.com/education/

Instructional materials for teaching bioinformatics. These include animated tutorials on topicssuch as BLAST, finding mutations in a protein, and graphing with MS-Excel.

Bioinformatics.fi

An international, two-year Master's programme jointly managed by the University of Tampere and the University of Turku, Finland.

Perlsource.net

Provides online courses in Perl programming for bioinformatic tools.

The Department of Informatics is a vacant position as a researcher in computer science, related to Computational Biology Unit (CBU), for 3 years.

The position is part of CBU Service Group and will focus on bioinformatic analysis project and especially the analysis of high-throughput data, including NGS (sequencing), and proteomics data.

The successful candidate will be part of the Norwegian bioinformatics platform's national helpdesk within the project ELIXIR.NO

Applicants must hold a PhD in a relevant subject such as computer science, mathematics, molecular biology and also possess expertise and experience in bioinformatics statistics and analysis of data from high-throughput molecular experiment.

Basic programming or scripting skills are required. Experience in Python, R, Perl, Linux-based operating systems and moreover knowledge of databases and web programming will be a strength for applicants.

We expect enthusiasm and independence and moreover the ability to work in an interdisciplinary team environment.

Good knowledge of English is required.

Salaries start at level 57 (code 1109/LR 24.1) by appointment. Further promotion occurs after
service seniority in the position (at grade 57-65). Of particularly highly qualified applicants may be considered a higher salary.

Further information about the position is available from the chair of the CBU,
Professor Inge Jonassen, e-mail: Inge.Jonassen @ ii.uib.no

The successful applicant must comply with the guidelines that apply at any given time the position.

State employment shall as far as possible reflect the diversity of the population. It is therefore an objective to achieve a balanced age and sex composition and the recruitment of persons with immigrant backgrounds. Persons with immigrant background are requested to apply for the position.

Women are particularly encouraged to apply. If the experts find that several applicants have approximately equivalent qualifications, the rules on equal in the Personnel Regulations for Academic Positions will be applied.

University of Bergen applies the principles of public openness when recruiting staff to scientific positions.

Information about the applicant may be made public even though the applicant has requested not to be named in the list of applicants. If the request does not host admitted to the result, the applicant shall be notified of this.

Send application, CV, certificates, diplomas, undergraduate work and a list of publications (list of publications) online by clicking on https://www.jobbnorge.no/jobbsoknet/login.aspx?returnurl=/jobbsoknet/jobapplication.aspx?jobid=95196

You need to upload certified translations into English or a Scandinavian language of appendices, such as diplomas and transcripts.

Applications sent by email to individuals at the institute will not be considered.

Deadline: 9 August 2013

Dated : 22 Nov 2013 -23 Nov 2013

http://www.ngsasia-congress.com/

You can also add your favourite NGS educational material, or workshop tutorial by commenting on this bookmarks for user benefit. 

Understanding the basics of genome sequencing:

Tutorial by Luke Jostins.

http://www.genetic-inference.co.uk/blog/2009/04/basics-sequencing-dna-part-1/

http://www.genetic-inference.co.uk/blog/2009/08/basics-sequencing-dna-part-2/

A window into third-generation sequencing

http://hmg.oxfordjournals.org/content/19/R2/R227.full.pdf

==============================================

NGS data analysis pipelines

• Detecting and annotating genetic variations using the HugeSeq pipeline  DOI: 10.1038/nbt.2134
• NARWHAL, a primary analysis pipeline for NGS data http://bioinformatics.oxfordjournals.org/cgi/content/abstract/28/2/284?etoc
• RseqFlow: Workflows for RNA-Seq data analysis  DOI: 10.1093/bioinformatics/btr441
• ngs_backbone: a pipeline for read cleaning, mapping and SNP calling using Next Generation Sequence  10.1186/1471-2164-12-285
• A framework for variation discovery and genotyping using next-generation DNA sequencing data  PubMed: 21478889
• SNiPlay: a web-based tool for detection, management and analysis of SNPs. Application to grapevine diversity projects  DOI: 10.1186/1471-2105-12-134 Abstract: http://www.biomedcentral.com/1471-2105/12/134/abstract
• WEP: a high-performance analysis pipeline for whole-exome data http://www.biomedcentral.com/1471-2105/14/S7/S11
• DDBJ read annotation pipeline: a cloud computing-based pipeline for high-throughput analysis of next-generation sequencing data. http://www.ncbi.nlm.nih.gov/pubmed/23657089
• GATK: a Toolkit for Genome Analysis http://www.broadinstitute.org/gatk/
• Metagenomics:http://www.nbic.nl/education/nbic-phd-school/course-schedule/ngsmetagenomics/
• RNASeq:http://www.nbic.nl/education/nbic-phd-school/course-schedule/ngsrnaseq/
• Bioinformatics and Seq courses: http://www.isb-sib.ch/training/training-activities-schedule/archive-2013.html
• Variant Detection (Model organism) Advanced tutorial https://docs.google.com/document/pub?id=1CuKkKylVDb03tnN7RSWl5EUzleetn0ctjmvaidPKLxM
• Variant Detection Introductory tutorial https://docs.google.com/document/pub?id=1ZRzrjjOCvtAu3m-IKL-rbJ1f4On60dDL_IEwG7oejdI
• Microbial de novo Assembly for Illumina Data Introductory tutorial https://docs.google.com/document/pub?id=1N3AB9ptISUu4zULqe1kXpVF0BDyGb5f5yzxWSJd_WNM
• RNAseq Differential Gene Expression Introductory tutorial https://docs.google.com/document/pub?id=1KbTiBHtvHLfPRZ39AY3uriazrINA8TJzgjjwn1zPP7Y

" Please add your favourite NGS link below in comment section for the benefit of bioinformatics community ". 

Address of the bookmark: http://chagall.med.cornell.edu/NGScourse/