Applications with complete bio-data from candidates possessing the required qualifications are invited for the posts of JRF (1) and Project Assistant (1) in DBT, GOI-funded research project “Next Generation Sequencing (NGS)- based de novo assembly of expressed transcripts and genome information of Orchids in North-East India” in DBT’s Twinning programme for NE as per DBT sanction order and norms.

(i) JRF(1 no.):

Qualifications: M.Tech/M.Sc in Life Sciences/ Botany/ Zoology/ Biochemistry/ Biotechnology/ Bioinformatics;

Desirable: Aptitude for Bioinformatics and Computer Programming/ Next generation sequencing data analysis

(ii) Project Assistant (1 no.):

Qualifications: Graduation in Science,

Desirable: Experience of working in a Life Science/Plant Biotechnology lab. and familiarity with computers and field work viz. collection of samples.

The applications through email bicnehu@gmail.com or post must reach the undersigned within 15 days from the date of publication of this advertisement. The advertised posts are purely temporary for the duration of the project and subject to availability of the funds from DBT. The appointment does not confer any entitlement or right over the posts for absorption in the University service. Prof. Pramod Tandon, PI/Mr. Devendra Kumar Biswal (Co-PI) email: bicnehu@gmail.com

Advertisement: www.nehu.ac.in/Advertisements/BIC_AdvtPV_030815.pdf

Address of the bookmark: https://github.com/CSB5/INC-Seq

Jawaharlal Nehru University has been granted funds by the Department of Biotechnology (DBT), Govt. of India to initiate an Inter-School programme in JNU to strengthen training and research called "DBT-Jawaharlal Nehru University, New Delhi-Interdisciplinary Life Science Programme for Advanced Research and education" with the broad project area entitled "From Molecules to Systems: Exploring biological space using chemical and synthetic biology" cutting across Physical, Chemical and Biological Sciences.

Applications are invited for the following purely temporary posts at various levels in the various Group projects for Research and Technical positions. The project is upto March 2017, but the appointments shall be initially for a period of one year, renewable every year depending on the performance of project staff:

Project Sub-Title: Synthetic Genomics: Making sense out of 'junk' DNA

Senior Research Fellow (SRF) - 01 Post

Qualifications: M.Sc in Bioinformatics, with minimum 2 year research experience, specialization in microRNA, molecular modelling, systems and/or Synthetic biology with publication in the relevant area would be desirable.

Investigator: Prof. Pawan Kumar Dhar

Fellowship: Rs. 14000+30% HRA p.m.

Project Sub-Title: "Structure, function, and dynamics of biomolecules and Molecular engineering"

Postdoctoral Fellow (PDF) - 01 Post

Essential Qualifications: PhD in Science(Bioinformatics/Computational Biology, Physics, Chemistry, Mathematics, & Statistics), specialized in the area of Computational Biology/Structural Bioinformatics/ Quantum Chemistry/Molecular Dynamics & Simulation /Systems Biology , reflected by thesis topics and or publication of papers during PhD and/or Post doctoral experience.

Desirable Qualifications: Computational methods and designing experience in the field of Structure based or ligand based drug design, Chemoinformatics, Programming capabilities as required for developing tools in the computational & systems Biology.

Investigator: Prof. Indira Ghosh, SCIS

Salary: Rs. 22, 000 + 30% HRA

(Note: Revised emoluments shall be payable if Educational Qualifications or Eligibility Criteria as per DST OM No. A.20020/11/97-IFD dated 31-03-2010 are met by the research personnel)

The applications on plain paper indicating name, date of birth/age, address, essential / technical / professional qualifications, experience, research work, should reach the Programme Coordinator on or before 27th August 2015 at the following address:

The Envelop should be marked for the Post applied for. Any clarifications regarding projects may be sought from the respective project investigators as mentioned.

Address for correspondence:
Programme Coordinator
DBT-JNU BUILDER programme
School of Biotechnology
Jawaharlal Nehru University
New Delhi 110067

More at http://www.jnu.ac.in/career/currentjobs.htm

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

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

The position is open for immediate appointment and available for two years and then extendable for additional one year. The applicant will be appointed as Research Associate based on qualifications as detailed below:

Research Associate:

-Master’s degree with bioinformatics with at least 2 years of research experience in Next Generation sequencing data analysis as evidence from Fellowship/ Associateship / Training / other engagements.

-Familiarity with bioinformatics tools, database development, programming skills

-Minimum 1 publication in any peer reviewed journal

Salary will be as per ICAR rules and guidelines. Application will be shortlisted based on CV, reference letters from mentors and telephonic interview. Candidates will be called for a personal interview at Bangalore before appointment. No travel expense will be provided for attending interview at Bangalore.

Interested candidates may send a Letter of Interest and CV by email to: keshav@ibioinformatics.org before September 29, 2015.

bwa aln hs37m.fa r1.fq > r1.sai && bwa aln hs37m.fa r2.fq > r2.sai \
&& bwa sampe hs37m r1.sai r2.sai r1.fq r2.fq > r12.bwa.sam

bwa bwasw ../index/bwa/hs37m.fa r12.fq > r12.bwasw.sam

gsnap -A sam -d hs37m r1.fq r2.fq > r12.gsnap.sam

novoalign -r Random -o SAM -f r1.fq r2.fq -i 500 50 -d hs37m-k14s3.novo > r12.novo.sam

smalt map -f samsoft -i 650 -o r12.smalt-k20s13.sam hs37m-k20s13 r1.fq r2.fq

stampy.py -g hs37m -h hs37m -o r12.stampy.sam -M r1.fq,r2.fq

soap -D hs37m.fa.index -a r1.fq -b r2.fq -l 32 -g 3 -u dummy -2 dummy -o r12.soap

Working with other members of the TNDRG you will analyse complex genomic and epidemiological datasets, evaluating which computational tools are most suitable. You will contribute to the generation of innovative tools for linking epidemiological and multilevel omics datasets, ensuring that computer programs are written in a form that other collaborators can use and expand.

You will have or be close to completion of a PhD in either: bioinformatics; neuroscience; machine learning; statistics; epidemiology; neurology; or other relevant field. You will have experience programming on either R, Matlab, Python, C++, Java or any other imperative, object oriented or functional language.

Please direct Informal enquiries to Dr Alejo Nevado-Holgado (alejo.nevado-holgado@psych.ox.ac.uk).

You will be required to upload a supporting statement explaining how you meet the selection criteria for the post, a CV, and details of two referees as part of your online application.

The closing date for applications is 12.00 midday on 2 September 2015. Interviews will be held on Tuesday 15 September 2015.

https://www.recruit.ox.ac.uk/pls/hrisliverecruit/erq_jobspec_version_4.jobspec?p_id=118696

Junagadh Agricultural University has given a recruitment notification to fill the posts of Senior, Junior Research Fellows in the establishment.

Name & No: of Posts:

1. Senior Research Fellow: 05
2. Junior Research Fellow: 05

Title of the Projects under Senior Research Fellow:

1. Molecular mapping of important traits and their transfer through marker assisted selection in Groundnut and cotton
2. Aflatoxin and its management in groundnut at Saurashtra region of Gujarat.
3. Improvement in Agricultural Production through nanotechnological inventions at Junagadh.
4. Synthesis and Characterisation of chitosan based NPK-Nano fertilizers

Title of the Projects under Junior Research Fellow:

1. Improvement in Agricultural Production Through Nanotechnological Inventions at Junagadh.
2. Synthesis and Characterisation of chitosan based NPK-Nano fertilizers

Required Eligibility Criteria:

1. Senior Research Fellow:

Age Limit: Candidates age must be maximum 35 years
Educational Qualification: M.Sc in Nanotechnology/Biotechnology/Bioinformatics
Salary: Rs. 16,000/- + HRA for first and second year, Rs. 18,000/- + HRA during third year

2. Junior Research Fellow:

Age Limit: Candidates age must be maximum 30 years
Educational Qualification: B.Sc or M.Sc degree in the field of Nanotechnology/Biotechnology
Salary: Rs. 9,600/- , Rs. 14,400/- p.m

Eligible candidates may attend the walk-in-interview on 10-09-2015 with necessary certificates of testimonials

Click Here for Detailed Recruitment Notification
http://www.jau.in/attachments/Advt/BiotechSRFJRF.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