BOL: Related items

Integrative Genomics Viewer (IGV) tutorial

Neel — Sat, 12 Jul 2014 15:16:23 -0500

The Integrative Genomics Viewer (IGV) from the Broad Center allows you to view several types of data files involved in any NGS analysis that employs a reference genome, including how reads from a dataset are mapped, gene annotations, and predicted genetic variants.

http://www.broadinstitute.org/igv/

Address of the bookmark: https://wikis.utexas.edu/display/bioiteam/Integrative+Genomics+Viewer+%28IGV%29+tutorial

COSMOS, our workflow management system for NGS data

Jit — Wed, 23 Jul 2014 07:29:14 -0500

COSMOS, our Python-based management system for implementing large-scale parallel workflows focusing on, but not restricted to, large-scale short-read "NGS" sequencing data is open-access published via Advance Access in Bioinformatics (Gafni et al. 2014). It is also available for download for non-commercial academic and research purposes at:

http://cosmos.hms.harvard.edu/.

Address of the bookmark: https://cosmos.hms.harvard.edu/

Pacasus: Correction of palindromes in long reads from PacBio and Nanopore

BioStar — Mon, 12 Nov 2018 05:26:48 -0600

Tool for detecting and cleaning PacBio / Nanopore long reads after whole genome amplification. Check the poster from the Revolutionizing Next-Generation Sequencing (2nd edition) conference in the source folder: https://github.com/swarris/Pacasus/blob/master/vib2017.pdf.

The prepint version is found on http://www.biorxiv.org/content/early/2017/08/09/173872

It uses the pyPaSWAS framework for sequence alignment (https://github.com/swarris/pyPaSWAS)

Address of the bookmark: https://github.com/swarris/Pacasus

CoLoRMap: Correcting Long Reads by Mapping short reads

Jit — Mon, 20 Aug 2018 14:17:05 -0500

Second generation sequencing technologies paved the way to an exceptional increase in the number of sequenced genomes, both prokaryotic and eukaryotic. However, short reads are difficult to assemble and often lead to highly fragmented assemblies. The recent developments in long reads sequencing methods offer a promising way to address this issue. However, so far long reads are characterized by a high error rate, and assembling from long reads require a high depth of coverage. This motivates the development of hybrid approaches that leverage the high quality of short reads to correct errors in long reads.We introduce CoLoRMap, a hybrid method for correcting noisy long reads, such as the ones produced by PacBio sequencing technology, using high-quality Illumina paired-end reads mapped onto the long reads. Our algorithm is based on two novel ideas: using a classical shortest path algorithm to find a sequence of overlapping short reads that minimizes the edit score to a long read and extending corrected regions by local assembly of unmapped mates of mapped short reads. Our results on bacterial, fungal and insect data sets show that CoLoRMap compares well with existing hybrid correction methods.The source code of CoLoRMap is freely available for non-commercial use at https://github.com/sfu-compbio/colormap

ehaghshe@sfu.ca or cedric.chauve@sfu.ca

Address of the bookmark: https://github.com/sfu-compbio/colormap

Orange-Bioinformatics 2.5.34

Robert M Willioms — Mon, 06 Oct 2014 12:51:37 -0500

Orange Bioinformatics extends Orange, a data mining software package, with common functionality for bioinformatics. The provided functionality can be accessed as a Python library or through a visual programming interface (Orange Canvas). The latter is also suitable for non-programmers.

Orange Bioinformatics provides access to publicly available data, like GEO data sets, Biomart, GO, KEGG, Atlas, ArrayExpress, and PIPAx database. As for the analytics, there is gene selection, quality control, scoring distances between experiments with multiple factors. All features can be combined with powerful visualization, network exploration and data mining techniques from the Orange data mining framework.

Address of the bookmark: https://pypi.python.org/pypi/Orange-Bioinformatics/2.5.34

Biinformamatics Lead at Google Life Sciences

Fri, 17 Oct 2014 02:24:55 -0500

Google Life Sciences is recruiting a technical lead with experience in bioinformatics and clinical bioinformatics, including for biomarker discovery projects such as the Baseline study.

Responsibilities

Lead teams of scientists in structuring, prototyping, and executing large-scale bioinformatic and other analysis.
Develop novel bioinformatics, statistical, data processing, pathway, data mining and other algorithms to identify biological signals and their clinical correlates in broad kinds of individual and population data.
Develop novel platform-level analytical tools for sequence-based assays (assembly, annotation, variant calling and interpretation, phasing, genome structure, etc.), expression assays (RNAseq and microarray), proteomics, and metabolomics.
Develop statistical models that robustly correlate complex laboratory-derived information with phenotypic and clinical information.
Create scientifically rigorous visualizations, communications, and presentations of results.

Reference @ https://www.google.com/about/careers/search#!t=jo&jid=62095001

MIT Computational Biology Group

Thu, 18 Dec 2014 14:47:01 -0600

My research group consists primarily of computer science graduate students and postdocs with expertise in algorithms, statistical inferences and machine learning, and sharing a passion for understanding fundamental biological problems.

We work in a highly interdisciplinary environment at the interface of Computer Science and Biology. Since its inception, our lab has eagerly engaged in collaborative research partnerships with biological and experimental collaborators, facilitated by our affiliation with the Broad Institute and the Computational and Systems Biology initiative (CSBi) at MIT, our participation in the Epigenome Roadmap, ENCODE, and modENCODE consortia, and by several other ongoing collaborations at MIT, Harvard, and the Harvard Medical School affiliated hospitals.

http://compbio.mit.edu/

Nicolas Corradi Lab

Tue, 26 May 2015 16:19:02 -0500

The goal of our research is to better understand the biology of microbial organisms of significant ecological, veterinary and medical importance.
To achieve this goal, our team combines the power of next generation DNA sequencing and bioinformatics with molecular biology and experimental procedures.

Main research topics:
- Comparative and Population Genomics of Plant Symbionts
- Parasite Genome Evolution
- Experimental Evolution of Microbial Symbionts and Parasites
- Phylogenomics of Early Branching Fungi

More at http://corradilab.weebly.com/

Research Associate, Project Fellow (Biological Sciences) at IGIB

Sun, 12 Jul 2015 07:57:27 -0500

Research Associate, Project Fellow (Biological Sciences)
Institute of Genomics & Integrative Biology (IGIB) - New Delhi, Delhi
Pay Scale: Rs. 22,000/- + 30 % HRA per month
Educational Requirements: PhD in any branch of Biological Sciences with specialization in Bioinformatics with at least one research paper in Science Citation Indexed (SCI) journal
Desired Skills: Knowledge of molecular dynamics simulations
Details will be available at: http://www.igib.res.in/sites/default/files/24July2015.pdf

Project Fellow (Biological Sciences) Pay Scale: Rs. 16,000/- + 30 % HRA per month
Educational Requirements: M.Sc./B.Tech in life sciences/Biological sciences with at least 55 % marks
Experience Requirements: Research experience.
Details will be available at: http://www.igib.res.in/sites/default/files/24July2015.pdf

No of Post: 01
How To Apply: 1. Please fill up the proforma by clicking on the following link HR Online Form. 2. Candidate cannot apply for more than two posts. Last date of receiving application is 12-07-2015. No application would be entertained with “result awaited” status or after due date. List of shortlisted candidates will be put up on CSIR-IGIB website. No TA/DA will be paid to the candidates to attend the interview. The engagement shall be as per guidelines of CSIR/Funding agency. Candidates will have an option to give reply in Hindi. Note: The shortlisted candidates, have to report at 09:00 AM at Mall Road Campus, Delhi – 110007 on the day of interview along with any Photo ID card, (without photo ID card interview will not be conducted). 3 copies of updated signed C. V. (clearly mentioning Date of Birth and Highest Qualification with percentage), Dissertation (if any), PhD thesis (if any) and original certificates/Self attested photocopies for verification.
Detail of Interview: 24 July, 2015 at 10:30 AM
Age Limit: 28 Years

RA Bioinformatics at Bharathidasan University

Fri, 17 Jul 2015 19:40:45 -0500

Applications are invited from individuals who have high motivation to do research for the DBT sponsored project o n “Establishment of National Repository for Microalgae & Cyanobacteria” funded by Department of Biotechnology, Govt. of India under the supervision of Dr. N. Thajuddin, Principal Investigator, Department of Microbiology, Bharathidasan University, Tiruchirappalli- 620 024.

1. Research Associate – 1 No.

Rs. 36,000/38,000/40,000 per month for I, II and III year + 20% HRA

Essential : Doctoral degree in relevant subject from recognized University/ Institutes

Desirable: Research experience in molecular biology and bioinformatics.

Interested candidates can send their complete CV in plain paper with a passport size photograph, with details of marks secured in all subjects from plus two stage (with proof, full postal address, sex, date of birth, community etc., along with additional qualification or experiences and two address of references whom could be contacted.

DEPARTMENT OF MICROBIOLOGY SCHOOL OF LIFE SCIENCES UNIVERSITY Dr. N. THAJUDDIN Professor & Head Dean, Faculty of Science, Technology & Engineering Tiruchirappalli – 620 024, India, Phone: +91 431 2407082; Mobile +91 098423 79719; E-mail: nthaju2002@yahoo.com

Application should reach the Principal Investigator on or before 5.8.2015 by Speed post/Couriers/Email (nthaju2002@yahoo.com), with subject printed as “Application for Research Associate /Technical Assistant /Lab attendant” in the envelop. Qualifying candidates will be short listed and communicated with date of interview. No TA and DA will be given for attending the interview. Address for Communication Dr.N.Thajuddin Principal Investigator Department of Microbiology Bharathidasan University Tiruchirappalli – 620 024, Tamil Nadu.

Advertisement: www.bdu.ac.in/adv/microbiology_advt.pdf