Main mission:

Develop and implement strategies for whole-genome sequencing of non-model
species
Generate high-quality de novo genome assemblies using short- and long-read
sequencing technologies
Perform genome annotation and structural/functional characterization
Conduct comparative genomic analyses across related species or populations
Design and implement genome-wide association studies (GWAS) to identify
loci associated with phenotypic or adaptive traits
Integrate genomic, phenotypic, and environmental datasets
Contribute to the development of reproducible bioinformatics pipelines

Activités (Activities):

Lead the genomic component of the research project
High-molecular-weight DNA extraction optimization
Long-read genome assembly (PacBio HiFi / ONT)
Genome polishing and quality assessment (BUSCO, QUAST)
Structural and functional annotation
Variant discovery (SNPs, indels, SVs)
Population genomic analyses (FST, demographic inference)
Mixed-model GWAS accounting for structure
Workflow development (Snakemake/Nextflow)
HPC-based pipeline implementation
Publish results in peer-reviewed journals
Present findings at international conferences
Collaborate with experimental and computational team members
Contribute to project development
Mentor graduate students when appropriate

More at https://evol.mcmaster.ca/brian/evoldir/PostDocs//MontpellierU.ComparativeGenomics

BioCoder features:

• Novel therapeutic discovery strategies
• Hardware such as low-cost lab equipment or diagnostics
• Open or low­-cost bioinformatics tools
• Engineered organisms for the production of small molecules, biologics, or other products
• Research projects at a community labspace or projects for science education or public engagement
• Hardware or software for lab automation
• Citizen science or DIY research projects
• Science policy
• Tools to increase reproducibility in research, or anything related

Address of the bookmark: https://www.oreilly.com/biocoder/

The following 5 questions are those that I have heard many times during the job-search process. There is no reason for not planning responses in such situations.

1. Tell Us About Yourself
This is a very typical opener in interviews. It's a perfect question to ask, and getting something planned will really help you concentrate and ease in the conversation. However, you need to make sure that your response is applicable to the job you're interviewing.
It's probably better to keep your answer professional. Try to include these in the answer as well: where did your love of science and bioinformatics come from? How the heck did you end up in this field? Why programming and scripting ?

2. What is your plan for your bioinformatics career? / How do you look at yourself in five years? / How are your personal objectives to accomplish these goals / What are the plan for your research fundings ?

Your CV/resume has already impressed the selection panel if you have been invited for an interview. The questions from the bioinformatics interview team provide an incentive for you to market yourself and illustrate the work in question with the most appropriate knowledge.

3. What do you understand about the job description/What would your suggested research path be if you were a successful candidate?
Summarize the specifics of the advertised bioinformatics position in your own words. Follow on with some suggestions of how you want to extend your research and create your own projects within the community.

4. Will you work as a group or do you want to work on your own?
This requirement can vary from jobs to job, so when addressing, be alert. A company/research PI may need a bioinformatician that is able to work on a single project autonomously, or they may need a person who can help direct and organize a team. In your response, refer to the job description.

5. What particular methods have you used to date with your experiments?
You might have experience with all the laboratory techniques described in the job description, but stress the ones you highly experienced with. Highlight your professional abilities and stress that you are extremely capable of mastering new techniques with others ...

At the end of the day, remember that you're questioning the jury as well as they're interviewing you. You will ought to think of any questions you would like the interview panel to pose. This indicates that you have done your homework and serious about the position.

All the best for your future job interview.

1. NCBI (National Center for Biotechnology Information):

   • NCBI provides various databases related to genetic information, including 16S rRNA sequences.
   • You can access the 16S ribosomal RNA sequences from NCBI's Nucleotide database (https://www.ncbi.nlm.nih.gov/nucleotide/).
   • Perform a search using keywords like "16S rRNA" or specific bacterial names to find relevant sequences.
   • You can download sequences individually or in batches using the provided tools.

2. GreenGenes:

   • GreenGenes is a widely used 16S rRNA gene sequence database.
   • You can access it at http://greengenes.secondgenome.com/.
   • GreenGenes provides precompiled databases for various purposes, including classification, alignment, and phylogenetic analysis.

3. SILVA:

   • SILVA (https://www.arb-silva.de/) is another comprehensive database for ribosomal RNA (rRNA) sequences.
   • It covers not only 16S rRNA but also other ribosomal RNA sequences.
   • SILVA provides precompiled databases for various purposes, including taxonomic classification and alignment.

4. Ribosomal Database Project (RDP):

   • RDP (http://rdp.cme.msu.edu/) is a curated database that offers 16S rRNA sequences.
   • It provides tools for sequence analysis and classification.
   • You can download sequences and taxonomy information from their website.

5. QIIME (Quantitative Insights Into Microbial Ecology):

   • QIIME (https://qiime2.org/) is a widely used bioinformatics platform for microbiome analysis.
   • It provides tools for analyzing microbial communities, including processing 16S rRNA sequences.
   • QIIME often includes its own preprocessed 16S rRNA databases that can be used for analysis within the platform.

Before downloading any database, make sure to read the terms of use and citation requirements, as some databases may have specific usage policies. Additionally, consider the compatibility of the database with your analysis pipeline and software tools.

NCBI 16s RNA database location ftp://ftp.ncbi.nih.gov/blast/db/16SMicrobial.tar.gz

http://www.gigasciencejournal.com/content/2/1/10/abstract

http://blogs.nature.com/news/2013/07/genome-assembly-contest-prompts-soul-searching.html

http://assemblathon.org/post/44431915644/feedback-and-analysis-of-the-assemblathon-2-p

View full lesson: http://ed.ted.com/lessons/james-watson-on-how-he-discovered-dna Nobel laureate James Watson opens TED2005 with the frank and funny story of how he and his research partner, Francis Crick, discovered the structure of DNA. Talk by James Watson.

More at file:///home/urbe/Downloads/diamond_manual.pdf

http://www.nature.com/nmeth/journal/v12/n1/full/nmeth.3176.html

Address of the bookmark: https://github.com/bbuchfink/diamond

Testing for similarities between DNA (deoxyribonucleic acid) samples from two people allows family relationships to be established – or disproved – to an extraordinarily high degree of certainty. A common use for a DNA test is to establish if a man is the biological father of a child; this is known as a paternity test. However, there are other uses for the science of DNA testing (also called genotyping), these include forensic analysis of human DNA samples, and tracking relationships amongst domesticated animals.

The order in which the bases occur in DNA is referred to as the DNA sequence. Each person is unique and just as people differ in their fingerprints, they also have a unique and slightly different DNA sequence. Half of a person’s DNA is received from their mother, and half is received from the father. However, while fingerprints have no value for establishing family relationships, the minor variations in DNA sequence are extraordinarily useful for this purpose. All cells of our body contain DNA, skin cells from the lining of the cheek provide a simple and convenient source of material.

DNA is purified from these cells and the minor variations are read out as a type of bar-code by a machine. When the net DNA ‘barcodes’ from family members are lined up next to each other it becomes clear when a child is related to biological parents because half the stripes in the bar-code like signature will line up with those of the mother, and half will line up with those of the father. On the other hand, in the absence of a biological relationship, the DNA signatures from a child and from a potential parent are not found to have 50% in common. It may be appreciated that DNA testing is the most convenient and scientifically accurate method of determining relationships between people.

Following are the list of companies who qssist in DNA testing:

DNA testing companies

• 23andMe (admixture, adoption, deep ancestry, genealogy) (health and trait reports also available in some countries)
• 24 genetics (admixture, exome sequencing, health, paternity, pharmacogenetics, whole genome sequencing) A company catering for the Spanish market
• African Ancestry (deep ancestry)
• AfricanDNA (FTDNA affiliate) (admixture, deep ancestry, genealogy)
• AncestrybyDNA (admixture, deep ancestry)
• AncestryDNA, a subsidiary of Ancestry.com (admixture, adoption, genealogy)
• Atlas Biomed (deep ancestry, diet, health and traits, sport) A test catering for the Russian market
• BritainsDNA (formerly Ethnoancestry) (admixture, deep ancestry)
• Centrillion Biosciences (aka TribeCode) (admixture, deep ancestry)
• CymruDNAWales - see BritainsDNA
• Dante Labs (exome sequencing, health, whole genome sequencing) A test aimed at the European market
• DNA Ancestry and Family Origin (FTDNA affiliate in the Middle East) (admixture, adoption, deep ancestry, full mtDNA sequencing, genealogy)
• DNA Consultants (admixture, deep ancestry)
• DNA Tribes (admixture)
• DNA Worldwide (formerly a FTDNA partner. See also Living DNA)
• Ethnoancestry - see BritainsDNA
• Family Tree DNA (admixture, adoption, deep ancestry, full mtDNA sequencing, genealogy, Y chromosome sequencing)
• Full Genomes Corporation (whole genome sequencing, Y-chromosome sequencing)
• Gene by Gene - the parent company of Family Tree DNA which now incorporates the companies previously known as DNA Traits, DNA DTC and DNA Findings (research, health, exome sequencing, whole genome sequencing)
• Genebase (deep ancestry, genealogy)
• GenoTek (admixture, genealogy, diet and fitness, family planning, health, talents and sports) A company catering for the Russian market
• Genographic Project (admixture, deep ancestry)
• Genos Research Inc (DTC whole exome sequencing; consumer focused healthcare big data spin out from Complete Genomics; Note: no genetic genealogy focus or tools)
• Guardiome (admixture, whole genome sequencing and interpretation)
• Helix (exome sequencing) US supplier of the Genographic Project Geno 2.0 Next Generation test
• iGENEA (FTDNA affiliate) (admixture, deep ancestry, genealogy)
• IrelandsDNA - See BritainsDNA (formerly Ethnoancestry)
• MyDNA Global - a new name for BritainsDNA
• Living DNA (admixture, deep ancestry) See also DNA Worldwide
• MyHeritage DNA (admixture, genealogy)
• Oxford Ancestors (deep ancestry)
• Roots for Real (admixture, deep ancestry)
• ScotlandsDNA - (formerly Ethnoancestry) (admixture, deep ancestry)
• Sorenson Genomics (laboratory services)
• Sure Genomics (whole genome sequencing and interpretation)
• TribeCode See Centrillion Biosciences
• Veritas Genetics (whole genome sequencing and interpretation)
• Xcode (Diet and Fitness, Precision medicine, Genotyping, Sequencing, Interpretation)
• YorkshiresDNA - See BritainsDNA (formerly Ethnoancestry)
• WeGene (admixture, deep ancestry, health, sports, traits) A test tailored for the East Asian market
• YSEQ (custom Y-SNPs, Y-STRs, SNP panels, whole genome sequencing)

Detail paper at https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-3927-8

Address of the bookmark: https://github.com/VicugnaPacos/ALPACA