BOL: Related items

Bioinformatics market in India

Rahul Agarwal — Fri, 23 Aug 2013 07:08:49 -0500

Key Topics Covered in the Report:

The market size of the Indian Bioinformatics Industry , FY’2007-FY’2013
Market segmentation of India bioinformatics industry by application by sectors, FY’2007-FY’2013
Market Segmentation of India bioinformatics industry by products and services,FY’2007-FY’2013
Market Segmentation of India bioinformatics industry by applications of bioinformatics ,FY’2007-FY’2013
India bioinformatics industry trends and developments
Government regulations and initiatives of India bioinformatics industry
Major bioinformatics research institutes in India
Market Share of leading players in bioinformatics industry in India,FY’2013
Company profiles of major players in India bioinformatics industry
Future outlook and projections on the basis of revenue in India bioinformatics market, FY’2014-FY’2018

(Source: Ken Research)

Address of the bookmark: http://www.kenresearch.com/healthcare/biotechnology/india-bioinformatics-industry-research-report/392-91.html

The Breitbart lab

Tue, 17 Sep 2013 18:19:49 -0500

Breitbart’s lab has created a new branch of biology called metagenomics in which one can sample and sequence genetic material collected from the environment.

Breitbart lab is located in the College of Marine Science at the University of South Florida. She is chosen as top "10 Brilliant" scientist by Popular Science magazine.
http://www.popsci.com/science/article/2013-09/mya-breitbart

Lab Link:
https://sites.google.com/site/breitbartgenomicslab/
http://www.marine.usf.edu/faculty/mya-breitbart.shtml

Key Bioinformatics Scientists

Rahul Agarwal — Wed, 09 Oct 2013 13:37:07 -0500

Address of the bookmark: http://www.iscb.org/iscb-leadership-a-staff-/officers-and-board-directors

Application Scientist in Strand LifeSciences Bangalore

Mon, 07 Apr 2014 08:17:32 -0500

Job Description
We are looking for a motivated application scientist to help evaluate, compare, and develop next generation sequencing (NGS) data analysis methods. The successful candidate should be able to quickly understand the state-of-art computational biology techniques, prototype them and perform benchmarking studies. The candidate must also be comfortable working with people from different disciplines and be able to present data analysis results in a clear and effective manner. The candidate is also expected to interact with customers as needed, write technical reports and publish new methods and/or data analysis findings in public forums.

Candidate Requirements:
A PhD in computer science, computational biology, Bioinformatics, or a related field, along with sufficient programming skills for prototyping. Experience with next generation sequencing data analysis is required. Candidates with MS degree but with relevant work experience can also be considered.

To Apply
To apply, please send your updated CV and cover letter to Dr. Rohit Gupta (rohit@strandls.com).

Source: http://www.strandls.com/application-scientist

Metagenomics role in antibiotic resistance

Rahul Agarwal — Mon, 02 Jun 2014 08:04:40 -0500

poRe: an R package for the visualization and analysis of nanopore sequencing data

Jit — Thu, 23 Nov 2017 09:55:57 -0600

Motivation: The Oxford Nanopore MinION device represents a unique sequencing technology. As a mobile sequencing device powered by the USB port of a laptop, the MinION has huge potential applications. To enable these applications, the bioinformatics community will need to design and build a suite of tools specifically for MinION data.

Results: Here we present poRe, a package for R that enables users to manipulate, organize, summarize and visualize MinION nanopore sequencing data. As a package for R, poRe has been tested on Windows, Linux and MacOSX. Crucially, the Windows version allows users to analyse MinION data on the Windows laptop attached to the device.

Availability and implementation: poRe is released as a package for R at http://sourceforge.net/projects/rpore/ . A tutorial and further information are available at https://sourceforge.net/p/rpore/wiki/Home/

Contact:mick.watson@roslin.ed.ac.uk

Address of the bookmark: https://academic.oup.com/bioinformatics/article/31/1/114/2365693

Ra assembler - a de novo DNA assembler for third generation sequencing data

biogeek — Wed, 27 Dec 2017 20:36:54 -0600

Integration of the Ra assembler - a de novo DNA assembler for third generation sequencing data developed on Faculty of Electrical Engineering and Computing (FER), Ruder Boskovic Institute (RBI) and Genome Institute of Singapore (GIS).

Ra is in development since 2014 in the form of several separate components that used to be run individually.
This project aims to ease the usage of Ra by integrating it into a complete de novo assembly tool.

Unlike other state-of-the-art assemblers, Ra does not have an error correction step. Instead, it relies on detecting overlaps using a very sensitive and specific overlapper ("graphmap -w owler", https://github.com/isovic/graphmap) and constructing and reducing an overlap graph (Ra layout, https://github.com/mariokostelac/ra).

Address of the bookmark: https://github.com/mariokostelac/ra-integrate/

Flye: Fast and accurate de novo assembler for single molecule sequencing reads

Jit — Fri, 04 May 2018 19:16:22 -0500

Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio and Oxford Nanopore Technologies. The algorithm uses an A-Bruijn graph to find the overlaps between reads and does not require them to be error-corrected. After the initial assembly, Flye performs an extra repeat classification and analysis step to improve the structural accuracy of the resulting sequence. The package also includes a polisher module, which produces the final assembly of high nucleotide-level quality.

Address of the bookmark: https://github.com/fenderglass/Flye

Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications.

Jit — Mon, 28 May 2018 09:41:39 -0500

Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs. Manta discovers, assembles and scores large-scale SVs, medium-sized indels and large insertions within a single efficient workflow.

Address of the bookmark: https://github.com/Illumina/manta

gSearch: a fast and flexible general search tool for whole-genome sequencing

Jit — Mon, 06 Aug 2018 17:19:15 -0500

gSearch compares sequence variants in the Genome Variation Format (GVF) or Variant Call Format (VCF) with a pre-compiled annotation or with variants in other genomes. Its search algorithms are subsequently optimized and implemented in a multi-threaded manner.

Address of the bookmark: http://ml.ssu.ac.kr/gSearch/index.html