• Draft assembly fasta file
• Interleaved linked reads file (Barcode sequence expected in the BX tag of the read header or in the form "@readname_barcode" ; Run Long Ranger basic on raw chromium reads to produce this interleaved file)

Address of the bookmark: https://github.com/bcgsc/ARCS/

Applications are invited for admission to the Ph.D. programme in the Department of Biophysics, Molecular Biology & Bioinformatics, University of Calcutta for the year 2014 from eligible candidates who would be placed under the departmental teachers or affiliated research supervisors for the pursuance of their Ph.D. programme.

Candidates are requested to download the Ph.D. admission test application form from the University website and apply in the prescribed proforma by paying Rs. 100/- through a challan available through different University Cash counters. The challan is to be duly forwarded through the Head, Department of Biophysics, Molecular Biology & Bioinformatics, University of Calcutta.

The completed application form with a copy of the paid challan is to be submitted to the office of the Department by April 16, 2014.

Syllabus for the Test: The questions for the admission test and interview will be based on topics in the following areas:

Mathematical methods, Molecular and Cellular Biophysics, Molecular and Cell Biology, Biochemistry, Genetics, Plant Biology, Developmental biology, Neurobiology, Biotechnology and Bioinformatics.

However, the interview will be primarily based on the research emphasis of the candidate. Candidates must clearly indicate the program in which they want to apply.

Date of Admission test : April 22, 2014 (Tuesday)

Date of publication of selection list for the interview : April 22, 2014(Tuesday)

Date of Interview : April 23, 2014 (Wednesday)

Number of vacancies for the Ph.D. programme : 12

Reservation policy will be followed as per rules.

Candidates with valid NET/GATE/M.Phil. or equivalent qualifications are not required to appear at the admission test but would need to qualify in the interview.

Advertisement:

http://www.caluniv.ac.in/admission%20notice/PHD_BIO_PHYSICS.pdf

By default, the program will generate whole-genome LTR-RT annotation and the LTR Assembly Index (LAI) for evaluations of the assembly continuity of the input genome. Users can also run LAI separately (see Usage).

Address of the bookmark: https://github.com/oushujun/LTR_retriever

Welcome to phylobabble.org, a discussion forum for phylogenetic theory and applications. The primary goal of this forum is to discuss best practice and new developments in phylogenetics. Although we do have a Troubleshooting category for getting feedback on analyses, this is not a help site for running phylogenetics programs.

A great place to chat about phylogenetics for researchers and the broader community of students and science-interested citizens. 

Address of the bookmark: http://phylobabble.org/

Like other indel callers, Scalpel works by performing de novo assembly of regions of interest, so that misalignment to the reference genome cannot obscure the presence of an insertion or deletion. Scalpel's innovation is to repeatedly check its assembly before comparing to the reference genome, to account for simple sequence repeats that are a regular source of error in indel calling. When Scalpel assembles an exon, it collects reads that map to that exon (including partial matches), splits them into k-mers, and creates a de Bruijn graph to span the exon; however, if it detects repeats in the map, it iteratively increases the size of the k-mers by one base until the repeats are eliminated. This ensures that the final assembly of the exon is highly accurate while minimizing compute time.

The Cold Spring Harbor team's validation of Scalpel, published over the weekend in Nature Methods, compares Scalpel's performance on a live whole exome against HaplotypeCaller and SOAPindel. The donor is an individual with serious neurological disorders, which may be linked to a high incidence of indels. One thousand indels from this individual's exome, called by one or more of the informatics pipelines, were selected for focused resequencing. This resequencing revealed a 77% true positive rate for Scalpel calls, dramatically better than the rates for either of the competing tools; Scalpel performed especially well with indels longer than five base pairs, a traditional weak point for indel callers.

Finally, the authors demonstrate Scalpel's use on a large set of genetic data from nearly 600 families who donated samples to the Simons Simplex Collection, a project of the Simons Foundation Autism Research Initiative. Scalpel found a very high enrichment for indels in children affected by autism, compared with their unaffected siblings, a pattern that persisted even after excluding common variants.

Scientists have reconstructed the genome of an ancient human who lived nearly 5,700 years ago in Southern Denmark from the birch pitch- an ancient tar-like substance.

By sequencing the sample, researchers not only discovered the ancient human DNA but also microbial DNA reflecting the oral microbiome of the person who chewed the pitch, along with plant and animal DNA that could be the recent meal she might have consumed.

The DNA sample is comparable in quality to well-preserved teeth and skull bones. The DNA suggests that the chewer was a female, most likely with dark skin, dark brown hair and blue eyes.

Algorithms scripts @ https://github.com/jschendel/bioinformatics-algorithms-coursera

Address of the bookmark: https://github.com/jorvis/biocode

Check out the detail at https://www.ncbi.nlm.nih.gov/nuccore/MN908947

WALK IN INTERVIEW

A walk-in Interview for the following position tenable at the Bioinformatics Infrastructure Facility (BIF), Department of Biotechnology, Alagappa University will be held at the Department of Biotechnology, Alagappa University, Karaikudi 630 003 on 15.05.2014 (Thursday) at 01:00 PM. This national facility is funded by the Department of Biotechnology, Ministry of Science and Technology, Government of India, New Delhi. The main objectives of the Centre involve teaching and research activities in bioinformatics/biotechnology.

RA (One Post):

Salary : Rs. 11000 p.m. plus admissible HRA

Qualification: M.Sc., in Bioinformatics/Biotechnology/Biophysics/Biochemistry/ Life Sciences

Interested candidates are encouraged to send their Curriculum Vitae by email to “sk_pandian@rediffmail.com” in advance. On the day of interview, the candidates must produce original certificates in proof of their educational qualification and experience and a recommendation letter from the Head of the Department/Institution where last studied/worked. Candidates who have already passed the required Degree alone are eligible to appear for interview. No TA&DA will be given for attending the interview.

Advertisement: http://www.alagappabiotech.org/Walk%20in%20interview.pdf

Address of the bookmark: https://phytozome.jgi.doe.gov/pz/portal.html