Address of the bookmark: https://github.com/marbl/MashMap

Address of the bookmark: https://hpcugent.github.io/easybuild/

https://github.com/ggonnella/rgfa

Address of the bookmark: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5103826/

Pondicherry University, Puducherry has been identified as a nodal agency by the Department of Biotechnology, Govt. of India to coordinate this examination along with nine centres namely,

Pune University, Pune;

Anna University, Chennai;

Bose Institute, Kolkata;

Institute of Bioinformatics & Applied Biotechnology, Bangalore;

North-Eastern Hill University, Shillong, University of Hyderabad, Hyderabad;

University of Kerala, Thiruvananthapuram;

Jawaharlal Nehru University, New Delhi and

Assam Agricultural University, Guwahati. 

In the BINC 2015 and 2016 examination, 23 candidates and five candidates were certified respectively. DBT has agreed to fund Research fellowships for all the BINC qualified Indian nationals to pursue Ph.D. in Indian Institutes/Universities.

Note that the candidate must possess a postgraduate degree(or equivalent) & meet the criteria of the institutes/universities in order to avail research fellowship.

In addition, cash prize of Rs. 10,000/- will be awarded to the top 10 BINC qualifiers.

More at http://www.pondiuni.edu.in/exams/binc/

• Bioinformatics - RSS feed of current and advance online publications
• Genome Research - current & advance
• Genome Biology - editors picks, latest, most viewed, most forwarded. (Hit the RSS icon under each tab).
• PLoS Genetics - new articles
• PLoS Computational Biology - new articles
• Nature Genetics - current TOC and AOP
• Nature Reviews Genetics - current TOC and AOP

• Bioinformatics
• BMC Bioinformatics
• Briefings in Bioinformatics
• Genome Biology
• Genome Research: current and AOP
• Microbiome
• Nature Genetics, current & AOP
• Nature Reviews Genetics, current & AOP
• Nucleic Acids Research
• PLOS Computational Biology
• PLOS Genetics

Blogs. Some of these blogs are very relevant to bioinfo jobs. Others are more personal interest.

• The OpenHelix Blog
• Ensembl blog
• Galaxy News
• Blue Collar Bioinformatics
• Homologus
• Golden Helix - our 2 SNPs
• Genomics Law Report
• R-bloggers (aggregates feeds from >350 blogs about R)
• Genomes Unzipped
• Jason Moore's Epistasis Blog
• 23andMe - the Spitoon

• Variance Explained: David Robinson’s blog (Data Scientist at Stack Overflow, works in R and Python).
• Global Biodefense: News on pathogens, outbreaks, and preparedness, with periodic posts on genomics and bioinformatics-related developments and funding opportunities.
• In between lines of code: Lex Nederbragt’s blog on biology, sequencing, bioinformatics, …
• Simply Statistics: A statistics blog by Rafa Irizarry, Roger Peng, and Jeff Leek.
• Bits of DNA: Reviews and commentary on computational biology by Lior Pachter (fair warning: dialogue here can get a bit heated!).
• Blue Collar Bioinformatics: articles related tool validation and the open source bioinformatics community.
• Microbiome Digest – Bik’s Picks: A daily digest of scientific microbiome papers, by Elisabeth Bik, Science Editor at uBiome.
• Living in an Ivory Basement: Titus Brown’s blog on metagenomics, open science, testing, reproducibility, and programming.
• Enseqlopedia: James Hadfield’s blog on all things NGS.
• Epistasis Blog: Jason Moore’s computational biology blog.
• RStudio Blog: announcements about new RStudio functionality, updates about the tidyverse, and more.
• nextgenseek.com: Next-Gen Sequencing Blog covering new developments in NGS data & analysis.
• RNA-Seq Blog: Transcriptome Research & Industry News.
• The Allium: We all need a little humor in our lives. Like The Onion, but for science.

Forums.

• Seqanswers - bioinformatics forum
• Seqanswers - RNA-Seq forum
• BioStar
• BOL

Project Title : “Integrating genome scale metabolic analysis of model plant pathogen Ralstonia solanacearum with RNAseq and fluxomics”

Essential qualification : M.Tech. in CSE/IT (With specialization in Computational Biology/Bioinformatics) or M.Sc. in Bioinformatics/Biosciences/Molecular Biology Biotechnology preferably with NET/GATE/BET. Candidates should have minimum 55 % mark both in 10th and 10+2 Science examinations and mathematics at 10+2 Science. Desirable: Preference will be given to the candidates having experience in computational analysis of genome sequences or similar projects.

No. of Post : 01

Remuneration : Rs. 25,000/- for the 1st two years and Rs. 28,000/- for the 3rd year for SRF and applicable to the candidate having post graduate degree in Basic Science with NET/GATE/BET qualification or post graduate degree in professional course. Rs. 12,000/- for the 1st two years and Rs. 14,000/- for the 3 rd year for SRF,

Age : 28 years

Duration : Three (03) years or till completion of the project or until further order, whichever is earlier.

Hiring Process : Walk - In
Job Role: Research/JRF/SRF

Walk-in-interview will be held on 17th February, 2017, 11.15 a.m. at the office of the Head, Department of Computer Science and Engineering, Tezpur University.

Interested candidates may appear before the interview board with original documents from 10th standard onwards and photocopies of mark sheets, certificates, testimonials, caste certificate (if applicable), experience certificate certificates of NET/GATE/BET or similar examination qualifications, any other testimonials and a copy of recent curriculum vitae (CV) on the day of interview.

More at http://www.tezu.ernet.in/ProjectWalkin/Advt-DoRD-CSE-SSS-20-295-112-A.pdf

python finisherSC.py destinedFolder mummerPath

If you are running on server computer and would like to use multiple threads, then the following commands can generate 20 threads to run FinisherSC.

python finisherSC.py -par 20 destinedFolder mummerPath

Sometimes, if the names of raw reads and contigs consists of special characters/formats, FinisherSC/MUMmer may not parse them correctly. In that case, you want to have a quick renaming of the names of contigs/reads in contigs.fasta or raw_reads.fasta using the following command.

    perl -pe 's/>[^\$]*$/">Seg" . ++$n ."\n"/ge' raw_reads.fasta > newRaw_reads.fasta
    cp newRaw_reads.fasta raw_reads.fasta
    perl -pe 's/>[^\$]*$/">Seg" . ++$n ."\n"/ge' contigs.fasta > newContigs.fasta
    cp newContigs.fasta contigs.fasta

Address of the bookmark: https://github.com/kakitone/finishingTool

You have a PhD in Computational Science, Bioinformatics, or equivalent, and expertise in analysis and modeling of human RNA-seq data, statistics, data mining and machine learning. Excellent communication skills in English (written and oral) is a must. Flexibility and willingness to work across multiple projects and technologies in a rapidly evolving scientific context is required.
Salary will depend on qualification and experience. Starting date: immediate.

Interested candidates should send to farina.cinthia@hsr.it:

1. CV (please show evidences of relevant titles, projects, courses, references, etc.)
2. One page with a list of research topics (i.e. ongoing projects)
3. earliest availability

4. 2-3 contact names