BOL: Related items

bedtools

Jit — Fri, 24 Feb 2017 04:50:44 -0600

Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. For example, bedtools allows one tointersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF. While each individual tool is designed to do a relatively simple task (e.g., intersect two interval files), quite sophisticated analyses can be conducted by combining multiple bedtools operations on the UNIX command line.

bedtools is developed in the Quinlan laboratory at the University of Utah and benefits from fantastic contributions made by scientists worldwide.

Address of the bookmark: http://bedtools.readthedocs.io/en/latest/index.html

FinisherSC: a repeat-aware and scalable tool for upgrading de novo assembly using long reads

Jit — Mon, 27 Feb 2017 09:49:45 -0600

FinisherSC, a repeat-aware and scalable tool for upgrading de novo assembly using long reads. Experiments with real data suggest that FinisherSC can provide longer and higher quality contigs than existing tools while maintaining high concordance.

Address of the bookmark: http://kakitone.github.io/finishingTool/

Bioinformatics walk-in-interview at Tezpur University

Thu, 02 Mar 2017 04:24:46 -0600

A walk-in-interview will be held on 09 March, 2017, 11.15 a.m. at the office of the Head, Department of Computer Science and Engineering, Tezpur University for one (01) temporary position of Junior Research Fellow (JRF) in the DBT, Govt. of India sponsored project entitled “Integrating genome scale metabolic analysis of model plant pathogen Ralstonia solanacearum with RNAseq and fluxomics” under Dr. Siddhartha Sankar Satapathy (ssankar@tezu.ernet.in), Associate Professor, Department of Computer Science and Engineering, Tezpur University.

Interested candidates may appear before the interview board with original documents from 10th standard onwards and photocopies of mark sheets, certificates, testimonials, caste certificate (if applicable), experience certificate certificates of NET/GATE/BET or similar examination qualifications, any other testimonials and a copy of recent curriculum vitae (CV) on the day of interview.

Essential qualification: M.Tech. in CSE/IT (With specialization in Computational Biology/Bioinformatics) or M.Sc. in Bioinformatics/Biosciences/Molecular Biology Biotechnology preferably with NET/GATE/BET.

Candidates should have minimum 55 % mark both in 10th and 10+2 Science examinations and mathematics at 10+2 Science.

Desirable: Preference will be given to the candidates having experience in computational analysis of genome sequences or similar projects.

Remuneration: Rs. 25,000/- (Rupees twenty five thousand) only + HRA as admissible per month for the 1st two years and Rs. 28,000/- (Rupees twenty eight thousand) only + HRA as admissible per month for the 3rd year for SRF and applicable to the candidate having post graduate degree in Basic Science with NET/GATE/BET qualification or post graduate degree in professional course. Rs. 12,000/- (Rupees twelve thousand) only + HRA as admissible per month for the 1st two years and Rs. 14,000/- (Rupees fourteen thousand) only + HRA as admissible per month for the 3 rd year for SRF, for the candidate without NET/GATE/BET qualification. HRA will not be provided if campus accommodation is availed.

Age: Candidate shall not be more than 28 years of age on the date of interview. Upper age limit may be relaxed up to 5 years in the case of candidate belonging to SC/ST/ OBC/Women/Differently abled.

Duration: Three (03) years or till completion of the project or until further order, whichever is earlier.

N.B. No TA/DA will be paid to the candidates for attending the interview. For further details please contact: Dr. S. S. Satapathy Associate Professor Department of Computer Science and Engineering Tezpur University, Napaam-784028 Email: ssankar@tezu.ernet.in Contact no.: +91-9435979648

More Info: www.tezu.ernet.in/ProjectWalkin/Advt-DoRD-CSE-SSS-20-295-188-A.pdf

MetaBAT: An Efficient Tool for Accurately Reconstructing Single Genomes from Complex Microbial Communities

Jit — Mon, 06 Mar 2017 03:44:34 -0600

MetaBAT, An Efficient Tool for Accurately Reconstructing Single Genomes from Complex Microbial Communities

Grouping large genomic fragments assembled from shotgun metagenomic sequences to deconvolute complex microbial communities, or metagenome binning, enables the study of individual organisms and their interactions. Here we developed an automated metagenome binning software, called MetaBAT, which integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency. Tested on both synthetic and real metagenome datasets, MetaBAT outperforms alternative methods in both accuracy and computational efficiency. Applying MetaBAT to an assembly from 1,704 human gut samples formed 1,634 genome bins (>200kb) in 3 hours, where 621 genome bins are >50% complete with <5% contamination from other species. Further analysis shows that the quality of these genome bins approaches manually curated genomes.

Address of the bookmark: https://bitbucket.org/berkeleylab/metabat

PhenoGram

Jit — Tue, 07 Mar 2017 08:35:12 -0600

With PhenoGram researchers can create chomosomal ideograms annotated with lines in color at specific base-pair locations, or colored base-pair to base-pair regions, with or without other annotation. PhenoGram allows for annotation of chromosomal locations and/or regions with shapes in different colors, gene identifiers, or other text. PhenoGram also allows for creation of plots showing expanded chromosomal locations, providing a way to show results for specific chromosomal regions in greater detail.

Address of the bookmark: http://ritchielab.psu.edu/software/phenogram-downloads

Linux Cheat Sheet

Jitendra Narayan — Tue, 09 Jul 2013 17:30:04 -0500

In an attempt to find a good Linux reference for bioinformatician and BOL readers, I was unsuccessful at finding a decent one on the Internet. So, we decided to make a cheat sheet for biological programmers.

Research Associate openings at IASRI, India

Fri, 10 Mar 2017 03:53:03 -0600

Research Associate (RA) Two (2)

Ph.D. in Bioinformatics/ Agricultural Statistics/ Statistics/ Computer Science/ Computer Application or equivalent or Master’s in Bioinformatics/ Agricultural Statistics/ Statistics/ Computer Science/ Computer Application or equivalent with 4 years or 5 years of Bachelor’s degree having 1st Division or 60% marks or equivalent overall grade point average, with at least two years of research experience as evidenced from fellowship/ associateship/ training/ other engagements.

Knowledge in System Biology/ Statistical and computational Genomics/ Bioinformatics
Knowledge in computer programming, LINUX OS.
Expertise in use of R/other Bioinformatics software

More at http://iasri.res.in/employment/2017/cabin_advertisement_RA_SRF_YP_Mar2017.pdf

Phenomics of Moisture Deficit Stress Tolerance and Nitrogen Use December 31, 2019

Research Associate (RA) Two (2)

Ph.D. in Bioinformatics/ Agricultural Statistics/ Statistics/ Computer Science/ Computer Application or equivalent or System Administrator/ Computer expert for database development, development of phenome data bank and virtual phenomics facility, data archiving and Efficiency in Rice and Wheat-Phase II (Funded by National Agricultural Science Fund, ICAR) Master’s in Bioinformatics/ Agricultural Statistics/ Statistics/ Computer Science/ Computer Application or equivalent with 4 years or 5 years of Bachelor’s degree having 1st Division or 60% marks or equivalent overall grade point average, with at least two years of research experience as evidenced from fellowship/ associateship/ training/ other engagements. maintenance; Development of image analysis algorithms, APIs and IAPs.

Knowledge in System Biology/ Statistical and computational Genomics/ Bioinformatics
Knowledge of programming in LINUX/R/Perl/JAVA/PHP/JSP and use of various software & tools.
December 31, 2019

Ph.D. in Bioinformatics/ Agricultural Statistics/ Statistics/ Computer Science / Computer Application or equivalent or Master’s in Bioinformatics/ Agricultural Statistics/ Statistics/ Computer Science/ Computer Application or equivalent with 4 years or 5 years of Bachelor’s degree having 1st Division or 60% marks or equivalent overall grade point average, with at least two years of research experience as evidenced from fellowship/ associateship/ training/ other engagements.

Knowledge of Statistical and Computational Genomics/ Bioinformatics.
Knowledge of programming in LINUX/R/Perl/JAVA/PHP/JSP and use of various software & tools.
March 31, 2020

Bioinformatics: Introduction to PERL

Archana Malhotra — Thu, 11 Jul 2013 09:49:37 -0500

This course is aimed at those new to programming and provides an introduction to programming using Perl. By the end of this course, attendees should be able to write simple Perl programs and to understand more complex Perl programs written by others. The course will be taught using the online Learning Perl materials created by Sofia Robb of the University of California Riverside. Further information is available.

Pacbio Long Reads Compatible Software and Tools

Archana Malhotra — Wed, 15 Mar 2017 14:19:01 -0500

The following software packages are known to be compatible with PacBio® data, in addition to PacBio's own SMRT® Analysis suite. All packages are believed to be open source or freely available for non-commercial use. See the individual project sites for up-to-date license information. A separate page lists commercial software.

Know of any other open source software for PacBio data? Email us.

Software categories:

Address of the bookmark: https://github.com/PacificBiosciences/DevNet/wiki/Compatible-Software

NGS & Bioinformatics Summit Europe

Sat, 13 Jul 2013 17:02:34 -0500

NGS & Bioinformatics Summit Europe

Conference

7th to 8th October 2013
Berlin, Germany

Website: https://www.gtcbio.com/conference/ngseurope-overview
Contact person: Kristen Starkey

We welcome you to join us at GTC’s NGS & Bioinformatics Summit Europe on October 7-8, 2013 in Berlin, Germany.

Organized by: GTC
Deadline for abstracts/proposals: 7th September 2013