Input

Jabba takes as input a concatenated de Bruijn graph and a set of sequences:

the de Bruijn graph should appear in fasta format with 1 entry per node, the meta information should be in the format:
>NODE
the set of sequences should be in fasta or fastq format. These sequences will be corrected (e.g. PacBio reads). The corrections will be written to a file Jabba fasta.
The output is a file in fasta format with corrections of the long reads, and additionally a file in the input format containing uncorrected reads.

https://github.com/biointec/jabba/wiki

https://almob.biomedcentral.com/articles/10.1186/s13015-016-0075-7

Address of the bookmark: https://github.com/biointec/jabba

Address of the bookmark: http://www.phrap.org/consed/consed.html

Spines

http://www.broadinstitute.org/science/programs/genome-biology/spines

Address of the bookmark: http://www.broadinstitute.org/science/programs/genome-biology/spines

Address of the bookmark: https://github.com/mkirsche/Jasmine

HiCdat is easy-to-use and provides solutions starting from aligned reads up to in-depth analyses. Importantly, HiCdat is focussed on the analysis of larger structural features of chromosomes, their correlation to genomic and epigenomic features, and on comparative studies. It uses simple input and output formats and can therefore easily be integrated into existing workflows or combined with alternative tools.

More at http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0678-x

Address of the bookmark: https://github.com/MWSchmid/HiCdat

• nodes, which are labeled by sequences and ids
• edges, which connect two nodes via either of their respective ends
• paths, describe genomes, sequence alignments, and annotations (such as gene models and transcripts) as walks through nodes connected by edges

Address of the bookmark: https://github.com/vgteam/vg

An NSF-funded REU to study Y-chromosome diversity and sex-biased dispersal in wild brown rats (Rattus norvegicus) is available in the Munshi-South Lab at Fordham University. Our lab is currently investigating rat evolution at scales ranging from landscape genetics of individual cities to global patterns of diversity. Development of resources for investigating Y-chromosome diversity will support many of these studies. The REU student will work with the lab to bioinformatically identify Y-chromosome SNPs, design SNPtype assays,
extract DNA, genotype samples, and analyze data.

We seek applicants interested in bioinformatics, evolutionary biology, and related disciplines. Applicants must have taken a college-level genetics course. This REU will require attention to detail, reliability, independence, and critical thinking.

This position is based at Fordham University's field station, the Louis Calder Center, in Armonk, NY. The Calder Center is located approximately 25 miles north of New York City in a protected woodland area. Housing
will be provided at the Calder Center for the duration of the REU (May 23 to Aug 12, 2016). Additionally, the student will receive a $6,000 stipend. The selected student will participate in professional development activities through the Calder Centers REU program, including presentation of results at a research colloquium at the end of the summer.

To apply, please send a one page personal statement about your scientific interests and how this REU will support your professional goals, unofficial transcripts including a list of Spring 2016 courses, and names of two professional references (including title, address, phone number, and email address) as a single pdf (with your last name in the file name) to Dr. Jason Munshi-South (jmunshisouth@fordham.edu).

Applications are due March 4th, 2016.

Jason Munshi-South

http://millslab.org/research.html

Bhubaneswar 751023

Advt No. 07/2016

Institute of Life Sciences (ILS), Bhubaneswar, an autonomous Institute of the Department of Biotechnology, Ministry of Science & Technology, Government of India engaged in advanced research invites applications from Indian nationals for the Ph.D. program. The main focus of the projects will be computational biology in the following areas.

S. No. Area of Research Principal investigator

1. Computational Cancer Biology Dr. Anshuman Dixit

2. Immunogenomics & Systems Biology Dr. Sunil Kumar Raghav

3. Chromatin remodeling and hematopoiesis Dr. Punit Prasad

Candidates are strongly encouraged to visit ILS webpage for detailed information, regarding the research activities of the above mentioned scientists.

Essential Qualifications:

(a) Eligibility: M.Sc., M.V.Sc., M.Pharm., M.S. Pharma. (with NET/GATE/GPAT/BINC/any other equivalent national level exam) or M.Tech with minimum of 60% marks (or equivalent grade point). Those awaiting final result may also apply.

Applications received after the last date will not be accepted. The envelope should clearly be superscribed with “Application for Ph.D. program (computational biology)”. Short-listed candidates selected for the interview will be published in the Institute website (www.ils.res.in).

Application Fees: Applicants except SC/ST candidates are required to send a non-refundable D.D. for Rs.100/- in favour of “Director, Institute of Life Sciences, Bhubaneswar” payable at Bhubaneswar along with duly filled-in application form by the date mentioned below. Director, ILS reserves the right to withdraw the procedure without assigning any reasons thereof.

Important dates: 

Last date of receiving applications: 24th June 2016 

Date of display of short-listed candidates and instructions on the Institute website: 30th June 2016 

Date of interview: The interview will be organized on 25th July 2016

Advertisement: https://www.ils.res.in/wp-content/uploads/2016/05/advt07-16.pdf

https://github.com/pditommaso/awesome-pipeline

Address of the bookmark: https://github.com/pditommaso/awesome-pipeline