BOL: Related items

ASAR: Advanced metagenomic Sequence Analysis in R

Jit — Mon, 09 Jul 2018 05:20:50 -0500

An interactive data analysis tool for selection, aggregation and visualization of metagenomic data is presented. Functional analysis with a SEED hierarchy and pathway diagram based on KEGG orthology based upon MG-RAST annotation results is available.

To read the manual, please click the link https://askarbek-orakov.github.io/ASAR/

Address of the bookmark: https://github.com/Askarbek-orakov/ASAR

Internships @ Indian Institute of Science

Sun, 02 Feb 2014 03:05:58 -0600

Internships available for Bachelors and Masters students

Each node will host student interns interested in pursuing a research career in mathematical or computational biology at institutions located in its region.

Eligibility: Bachelors (3rd or 4th year) and Masters students

Average duration: 3 months (could be more in certain cases). These internships can be availed at any time during 2014 subject to consent from the faculty mentor.

Fellowship amount: Rs. 10,000 per month. In addition, outstation interns can receive up to Rs. 5000 per month for accommodation and Rs. 3000 for travel from and to their home place.

Application procedure: Apply online at http://nnmcb.appzone.co.in/

Deadline: February 10, 2014

Contact Information:

National Network for Mathematical and Computational Biology

Department of Mathematics

Indian Institute of Science

Bangalore 560 012

Tel: 080-2293 2893

Email: nnmcb@math.iisc.ernet.in

BASE: a practical de novo assembler for large genomes using long NGS reads

Rahul Nayak — Fri, 19 Oct 2018 07:25:21 -0500

new de novo assembler called BASE. It enhances the classic seed-extension approach by indexing the reads efficiently to generate adaptive seeds that have high probability to appear uniquely in the genome. Such seeds form the basis for BASE to build extension trees and then to use reverse validation to remove the branches based on read coverage and paired-end information, resulting in high-quality consensus sequences of reads sharing the seeds. Such consensus sequences are then extended to contigs.

Address of the bookmark: https://github.com/dhlbh/BASE

RCB Gurgaon Bioinformatics RA/PA Openings

Thu, 27 Feb 2014 08:42:15 -0600

Advt. No.1/2014

Recruitment for Research Associate and Project Assistant positions

Regional Centre for Biotechnology (RCB) is an autonomous academic institution established by the Department of Biotechnology, Govt. of India with regional and global partnerships synergizing with the programmes of UNESCO as a Category II Centre. The primary focus of RCB is to provide world class education, training and conduct innovative research at the interface of multiple disciplines to create high quality human resource in disciplinary and interdisciplinary areas of biotechnology in a globally competitive research milieu.

Research Associate (02 Position)

Consolidated emoluments Rs.22000/- + 30% H.R.A. p.m.

Essential: Ph.D. in Natural Sciences, minimum 60% marks in all qualifying exams and below 35 years of age.

Desirable: Prior experience at the PhD level in Biochemistry, Bioinformatics and Proteomics with a strong motivation for a career in research is highly desirable.

Strong PhD level training with proteins chemistry, protein purification and statistical analysis of proteomics or genomics dataset will be preferred. Either/ both qualifications should be substantiated by published papers.

Inter-Institutional Program for Maternal, Neonatal and Infant Sciences: A translational approach to studying preterm birth.

Principal Investigator: Dr. Dinakar M. Salunke

Applicants may apply along with the requisite documents (attested copies) pertaining to proof of date of birth, academic/professional qualifications, experience (if any), in the prescribed format available on our websites: www.rcb.res.in and www.rcb.ac.in. Applications should be sent to the Registrar, Regional Centre for Biotechnology, 180 Udyog Vihar Phase 1, Gurgaon-122016, Haryana, India, through Registered Post on or before Feb 28, 2014. A soft copy of the application should be sent by email to registrar@rcb.res.in. Incomplete applications or applications received after Feb 28, 2014 will not be entertained.

More at https://www.rcb.res.in/Advt-1._for_websites_PTB-revised.pdf

nQuire: A statistical framework for ploidy estimation using NGS short-read data

Jit — Thu, 31 Jan 2019 05:12:19 -0600

nQuire implements a set of commands to estimate ploidy level of individuals from species, where recent polyploidization occurred and intraspecific ploidy variation is observed. Specifically, nQuire uses next-generation sequencing data to distinguish between diploids, triploids and tetraploids, on the basis of frequency distributions at variant sites where only two bases are segregating.

For more background see also the publication at BMC Bioinformatics.

https://github.com/clwgg/nQuire

Address of the bookmark: https://github.com/clwgg/nQuire

Update Genome Workbench 2.7.15 released

Surabhi Chaudhary — Wed, 26 Feb 2014 16:12:17 -0600

NCBI Genome Workbench is an integrated application for viewing and analyzing sequence data. With Genome Workbench, you can view data in publically available sequence databases at NCBI, and mix this data with your own private data.

Genome Workbench can display sequence data in many ways, including graphical sequence views, various alignment views, phylogenetic tree views, and tabular views of data. It can also align your private data to data in public databases, display your data in the context of public data, and retrieve BLAST results.

Genome Workbench is built on the NCBI C++ ToolKit and uses cross-platform APIs for graphics. It runs on your local machine, and is available for Windows 2000/XP, Linux, MacOS X, and various flavors of Unix.

NCBI Genome Workbench is an integrated application for viewing and analyzing sequence data. Genome Workbench was developed entirely in-house at NCBI and makes use of the NCBI C++ ToolKit. The C++ ToolKit provides a convenient and flexible cross-platform API for managing system internals, database connections, network sockets, and the NCBI data model. In addition, the C++ ToolKit provides the Object Manager, which abstracts handling of sequences and sequence-related objects.

New Features in Genome Workbench 2.7.15

Multiple Alignment View: implemented adaptive feature display when zooming in
Active Objects Inspector replaces Selection Inspector. New View should offer an improved selection context examination. See Using Active Objects Inspector tutorial for more details.
Binary packages for Linux OpenSUSE 13.1 are now available

Bug Fixes and Improvements in Genome Workbench 2.7.15

Fixed major issue with OpenGL overlay/scrolling. Could cause crashes or view scrolling irregularities
Multiple Pane View: fixed crash on loading BLAST results
Graphical Sequence View: fixed crash on zooming in and out, related to SNP track
Graphical Sequence View: fixed Go To Position dialog to give better diagnostics in case of a user error
Graphical Sequence View: PDF export fixed rendering of Markers with commas in the name
Text View / Flat File: fixed Mac OS rendering issues
Text View / Flat File: performance optimization, extended capabilities of real-time rendering of molecules to tens of thousands
File Import: optimization improvement to speed up load of files containing multiple project items
File Import: remapping stage now shows accession.version and description of molecules, instead of plain GI numbers
Mac OS: improved tooltips for toolbar buttons
Phylogenetic Tree Builder Tool: improved diagnostics of errors
Multiple Alignment View: optimizations to avoid main GUI freezes
Open Dialog: removed duplicate elements in table of genomes (load Genome)
PDF export: fixed issue with XREF table errors
Tree View: fixed issues with showing Force Layout progress on Mac OS
Tree View: PDF export fixed issues for showing labels of collapsed nodes
Tree View: added an option to stop layout
Tree View: broadcasting mechanism fixed not to accumulate selected nodes

Reference:

NCBI news

http://www.ncbi.nlm.nih.gov/tools/gbench/

ClinCNV: Detection of copy number changes in Germline/Trio/Somatic contexts in NGS data

Neel — Thu, 16 Jan 2020 23:16:02 -0600

ClinCNV detects CNVs in germline and somatic context in NGS data (targeted and whole-genome). We work in cohorts, so it makes sense to try ClinCNV if you have more than 10 samples (recommended amount - 40 since we estimate variances from the data). By "cohort" we mean samples sequenced with the same enrichment kit with approximately the same depth (ie 1x WGS and 30x WGS better be analysed in separate runs of ClinCNV). Of course it is better if your samples were sequenced within the same sequencing facility.

Address of the bookmark: https://github.com/imgag/ClinCNV

Junior Research Fellow at IARI

Mon, 10 Mar 2014 13:10:56 -0500

DIVISION OF NEMATOLOGY
INDIAN AGRICULTURAL RESEARCH INSTITUTE
NEW DELHI 110012

Applications are invited for the posts of one Junior Research Fellow in the DBT funded project entitled “Plant parasitic nematode genome informatics - insilico resource development”. The project is for a period of three years.

Essential qualifications for JRF: First class M. Sc. / M. Tech in Bioinformatics. Knowledge of programming language, pearl, Statistics and database – HTML, CSS, Java script.

Desirable qualifications: Experience in handling next generation sequencing data

Age limit: 35 years maximum (5 year relaxation for SC/ST and women candidates) Emoluments: 16,000 + 30% HRA.

The post is purely temporary in nature and is co-terminus with the project. The appointment would be initially for one year and may be extended further upon satisfactory performance.

Those who are interested in pursuing Ph.D with strong research aptitude are preferred.

Interested candidates may attend the Walk in interview on 25th March 2014 along with the duly filled application forms (format in the following page) with all the relevant documents.

Venue: Division of Nematology, Indian Agricultural Research Institute, New Delhi 110012 (Room No. 306, 3rd floor, LBS building)

Reporting Time: Interested candidates should report strictly between 10.00 to 10.30 AM.

Interview time: 10.30 AM

Short-listed candidates will be called for interview at New Delhi. However, no TA and DA will be paid for attending the interview.

https://www.iari.res.in/files/JRF_Nema-07032014-20140307-170017.pdf

LoFreq*: A sequence-quality aware, ultra-sensitive variant caller for NGS data

BioStar — Tue, 18 Feb 2020 03:24:22 -0600

LoFreq* (i.e. LoFreq version 2) is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It makes full use of base-call qualities and other sources of errors inherent in sequencing (e.g. mapping or base/indel alignment uncertainty), which are usually ignored by other methods or only used for filtering.

https://github.com/CSB5/lofreq

http://csb5.github.io/lofreq/installation/

https://github.com/CSB5/lofreq/tree/master/dist

Address of the bookmark: http://csb5.github.io/lofreq/

Bioinformatic/computational postdoc at South Dakota State University

Wed, 12 Mar 2014 10:02:30 -0500

We seek an enthusiastic postdoctoral researcher to work with the Plant Science team within the Biochemical Spatio-temporal NeTwork Resource (BioSNTR). Bio-SNTR

is a state-funded virtual research center aimed at promoting imaging and informatics research infrastructure in South Dakota. BioSNTR research foci include analysis of large-scale genomics and imaging data, application of novel microscopy technologies to study signaling pathways, and identification of new compounds to manipulate signaling pathways.
Responsibilities: This person will be part of Plant Science team with research focus in bioinformatic and molecular network analyses of high throughput data (transcriptomic, proteomic, metabolomics, miRNA). The individual will be integrated into functional genomic projects encompassing grapevine dormancy and freezing tolerance (Fennell) and regulation of soybean nodulation (Subramanian). The successful candidate will perform computational analysis of high throughput, next-generation sequence data and possess the ability to use bioinformatics analytical tools on HPC clusters.

Required Qualifications:
• Ph.D. in plant computational biology or bioinformatics.
• Experience in a high performance computing environment.
• Perl, Python and Java programming experience
• Data management and database development experience

Desired Qualifications:
• Parallel computing experience
• Experience working in a multidisciplinary environment

Contact Information
South Dakota State University
Plant Science
Anne Fennell
anne.fennell@sdstate.edu
Tel. Number: 605-688-6373
http://www.biosntr.org