BOL: Related items

Picard

Neel — Fri, 29 Apr 2016 08:21:54 -0500

Picard is a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. These file formats are defined in the Hts-specs repository. See especially the SAM specification and the VCF specification.

Note that the information on this page is targeted at end-users. For developers, the source code, building instructions and implementation/development resources are available on GitHub.

The Picard toolkit is open-source under the MIT license and free for all uses.

Enjoy!

Address of the bookmark: http://broadinstitute.github.io/picard/

Post-Doctoral Fellow Jobs opportunity in SRM University

Thu, 17 Mar 2016 11:20:14 -0500

Post-Doctoral Fellow Jobs opportunity in SRM University

Essential qualification : Ph.D. in Bioinformatics/Biotechnology/Genetics/Computational Biology.Understanding of genomics data and advanced knowledge of Java, and C/C++ as the programming languages and the scripting language like perl and/or Python, SQL is preferred. Experience in High Performance Computing, data architecture, database development is desirable

Fellowship: Rs 35,000 /-

How to apply

Candidates are requested to send their CV, and a brief summary of research experience by e-mail careers.genetics@ktr.srmuniv.ac.in on or before 30/03/2016.

More at http://www.srmuniv.ac.in/jobs-applications-for-position-of-post-doctoral-fellow

SRF at NRCPB, New Deslhi

Fri, 25 Mar 2016 04:53:11 -0500

NRCPB Recruitment 2016 – Walk in for SRF & Young Professional Posts: National Research Centre on Plant Biotechnology (NRCPB) has announced a notification for the recruitment of Senior Research Fellow & Young Professional Scheme vacancies for the project “NPTC Co-ordinating Cell” on temporary & co-terminus basis. Eligible candidates may walk in interview on 29-03-2016 at 10.00 AM. Other details like age limit, educational qualification, selection process & how to apply are given below…

NRCPB Vacancy Details:
Total No.of Posts: 02
Name of the Posts:
1. Senior Research Fellow: 01 Post
2. Young Professional Scheme: 01 Post

Age Limit: Candidates maximum age should be 35 years. Age relaxation 5 years for SC/ ST/ OBC and women candidates as per ICAR rules.

Educational Qualification: Candidates should posses M.Sc/ M.Tech/ M.C.A. in Molecular Biology/ Biotechnology/ Life Sciences/ Allied Sciences/ Agricultural Sciences/ Computer Science/ Bioinformatics with 1st division or 60% marks or equivalent.

Selection Process: Candidates will be selected based on interview.

How to Apply: Eligible candidates may attend the interview along with four copies of biodata, original certificates, attested photocopies of each of the certificates and an attested copy of recent passport size photograph at NRCPB, LBS Building, Pusa Campus, New Delhi- 110012 on 29-03-2016 at 10.00 AM.

Important Dates:
Date & Time of Interview: 29-03-2016 at 10.00 AM.
Venue: NRCPB, LBS Building, Pusa Campus, New Delhi-110012.

Read more: http://www.nrcpb.res.in/content/walk-interview-srf-and-yp

One-Year Internship In Computational Biology & Bioinformatics

Mon, 04 Apr 2016 05:35:57 -0500

This one-year internship program has an inter-disciplinary curriculum that rests on research strengths and infrastructure at the computational biology & bioinformatics facility at Rajiv Gandhi Centre for Biotechnology . Using live demonstration platforms of high end genomic analysis systems including next generation sequencing, advanced proteomics platforms, advanced bio-imaging, student seminars in addition to computer laboratory based courses, interns will get state of the art exposure and training in application of bioinformatics to biomedical research.The internship involves 8 months of hands on training in wet and dry laboratory methods and a four-month dissertation. This internship program is designed for students who would like to gain good knowledge and experience in Bioinformatics as a prelude to taking up a PhD course or look for employment opportunities. The subjects covered during the internship will include but not limited to:
• Systems Biology
• Genomic Informatics
• Proteomic Informatics
• Biomedical Text Mining
• Ontologies
• Data Integration
• Data Mining
• Protein Structure & Function
• Metabolomics
• Molecular Evolution
• Pathways & Networks
• Resource Development
• Scripting & Algorithms
Qualifications: Admission to the Internship requires a first class degree in Engineering Sciences (Biotechnology/Computer Science), Medical/Dental/Pharmaceutical Sciences (MBBS or BDS or BAM or B.Pharm) or a Masters degree in Life Science, Medical Laboratory Technology, Biotechnology, Bioinformatics or Computer Science.
Internship Fees: The internship fee for the 12-month program is Rupees 70,000 (Rupees Seventy thousand). This is payable as an initial admission fee of Rs. 10,000 followed by payments of Rs. 6,000 monthly from months 3 to 9. The final completion certificate will be given after payment of all fees.
Mode of Selection: Selection will be based on interview and the top 5 candidates will be shortlisted for the program.
Location: Thiruvananthapuram

More at http://rgcb.res.in/TrainingPrograms/internship.php

Sequence assembly with MIRA 4

Priya Singh — Wed, 06 Apr 2016 08:21:22 -0500

MIRA is a multi-pass DNA sequence data assembler/mapper for whole genome and EST/RNASeq projects. MIRA assembles/maps reads gained by

electrophoresis sequencing (aka Sanger sequencing)
454 pyro-sequencing (GS20, FLX or Titanium)
Ion Torrent
Solexa (Illumina) sequencing
(in development) Pacific Biosciences sequencing

into contiguous sequences (called contigs). One can use the sequences of different sequencing technologies either in a single assembly run (a true hybrid assembly) or by mapping one type of data to an assembly of other sequencing type (a semi-hybrid assembly (or mapping)) or by mapping a data against consensus sequences of other assemblies (a simple mapping).

The MIRA acronym stands for Mimicking Intelligent Read Assembly and the program pretty well does what its acronym says (well, most of the time anyway). It is the Swiss army knife of sequence assembly that I've used and developed during the past 14 years to get assembly jobs I work on done efficiently - and especially accurately. That is, without me actually putting too much manual work into it.

More at http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html

Address of the bookmark: http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html

Understanding Fastqc Output

Jit — Fri, 15 Apr 2016 05:47:40 -0500

Understanding Following table and graphs

Duplication level
kmer profile
per base GC content
per base N content
per base quality
per base sequence content
per sequence GC content
per sequence quality
sequence length distribution

More at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/

Address of the bookmark: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/

CANU: Assembling Large Genomes with Single-Molecule Sequencing and Locality Sensitive Hashing.

Jit — Tue, 26 Apr 2016 11:38:10 -0500

Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing (such as the PacBio RSII or Oxford Nanopore MinION). The software is currently alpha level, feel free to use and report issues encountered.

Canu is a hierachical assembly pipeline which runs in four steps:

Detect overlaps in high-noise sequences using MHAP
Generate corrected sequence consensus
Trim corrected sequences
Assemble trimmed corrected sequences

Read the documentation

New release https://github.com/marbl/canu/releases

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

Bioinformatics Faculty at TNU

Wed, 27 Apr 2016 10:07:15 -0500

TNU is hiring faculty as Professors, Associate Professors and Assistant Professors in the following research and teaching programs.

Basic Sciences

Biotechnology & Bioinformatics

Qualifications are as per UGC norms. Please visit www.ugc.ac.in.

Educational, Age and experience requirements will be relaxed in exceptional cases.

Interested candidates are requested to apply with their complete CV with list of Publications, Patents, Industry and teaching experience at Undergraduate and Postgraduate level along with other relevant information to hr@tnu.in

Provide names and contact details of at least two references for confidential evaluation.

We follow Central University pay scales and few additional perks.

TNU follows highly liberal HR Policy with no salary constraint for exceptional candidates.

Applications are invited for the positions of - Professor, Associate Professor & Assistant Professor.
https://drive.google.com/file/d/0B0Y1Fpxmzyd3OHQ3aUNYa3hZY2c/view?usp=sharing

Reference
- Times of India, Ascent as on 20.04.2016.

YASS :: genomic similarity search tool

Jit — Mon, 02 May 2016 09:26:00 -0500

YASS is a genomic similarity search tool, for nucleic (DNA/RNA) sequences in fasta or plain text format (it produces local pairwise alignments). Like most of the heuristic pairwise local alignment tools for DNA sequences (FASTA, BLAST, PATTERNHUNTER, BLASTZ/LASTZ, LAST ...), YASS uses seeds to detect potential similarity regions, and then tries to extend them to local alignments. This genomic search tool uses multiple transition constrained spaced seeds that enable to search more fuzzy repeats, as non-coding DNA/RNA. Another simple, but interesting feature is that you can specify the seed pattern used in the search step (as provided for example by iedera).

Main features of YASS are:

multiple, possibly overlapping seeds and a new hit criterion to ensure a good sensitivity/selectivity trade-off
transition-constrained spaced seeds to improve sensitivity (transition mutations are purine to purine [A<->G] or pyrimidine to pyrimidine [C<->T])
using different scoring schemes with bit-score and E-value evaluated according to the sequence background frequencies
parameterizable output filter for low complexity repeats
reporting of various alignment statistical parameters (mutation bias along triplets, transition/transversion)
post-processing step to group gapped alignments

Address of the bookmark: http://bioinfo.lifl.fr/yass/

Supposedly Educational R

Rahul Nayak — Tue, 03 May 2016 16:43:08 -0500

R 3.3.0 (codename “Supposedly Educational”) was released today. You can get the latest binaries version from here. (or the .tar.gz source code from here). The full list of new features and bug fixes is provided below.

If you are using Windows you can easily upgrade to the latest version of R using the installr package. Simply run the following code in Rgui:

install.packages("installr") # install 
setInternet2(TRUE)
installr::updateR() # updating R.

Running “updateR()” will detect if there is a new R version available, and if so it will download+install it (etc.). There is also a step by step tutorial (with screenshots) on how to upgrade R on Windows, using the installr package. If you only see the option to upgrade to an older version of R, then change your mirror or try again in a few hours (it usually take around 24 hours for all CRAN mirrors to get the latest version of R).

I try to keep the installr package updated and useful, so if you have any suggestions or remarks on the package – you are invited to open an issue in the github page.