BOL: Related items

RA Bioinformatics at ICGED

Sun, 28 Jun 2015 12:24:01 -0500

Research Associate Position at ICGEB, New Delhi with Dr. Amit Sharma

Starting 15th July 2015, the position relates to a project specifically for in silico drug docking, screening, design, optimisation and linkage with active chemists.

Experience in many docking softwares and operating systems is essential.

Additional experience in bioinformatics and computational biology tools will be useful.

Submit curriculum vitae to: sb.icgeb@gmail.com

Closing date: 5 July 2015

Common steps for reads mapping !

BioStar — Thu, 09 Mar 2023 02:48:02 -0600

Mapping reads to a reference genome is an essential step in many types of genomic analysis, such as variant calling and gene expression analysis. Here are some general steps to follow for mapping reads to a genome:

Choose a read mapper: There are many read mappers available, such as BWA, Bowtie, and HISAT2. Choose a mapper that is appropriate for your type of data and research question.
Index the reference genome: Before mapping reads, the reference genome needs to be indexed. This involves creating an index of the genome sequence that allows the mapper to quickly find matches to the reads. Most mappers have their own indexing tools.
Prepare the read data: The reads should be in a format that is compatible with the mapper. Most mappers accept FASTQ or BAM files. Depending on the quality of the data, it may need to be filtered or trimmed before mapping.
Run the mapper: The mapper is run with the command-line interface or using a graphical user interface. The specific command depends on the mapper being used, but typically involves specifying the input data, reference genome, and output file format.
Evaluate the mapping results: After the mapping is complete, the results should be evaluated. This includes assessing the quality of the mapping, such as the mapping rate, the number of mapped reads, and the mapping quality score.
Post-processing: Depending on the analysis being performed, post-processing of the mapped reads may be necessary. This can include filtering reads based on quality, removing duplicate reads, and calling variants.

Overall, mapping reads to a reference genome is a complex process that requires careful consideration of the type of data, the research question, and the specific mapper being used.

1mb long DNA with Nanopore technology

Jit — Tue, 19 Dec 2017 18:49:28 -0600

The first continuous DNA read of more than a million bases (>1Mb) has been achieved, using Oxford Nanopore sequencing technology. Congratulations to Martin Smith and collaborators! Read more: http://bit.ly/2j5TNCO

Research Associate Bioinformatician @ University of Bristol

Wed, 26 Aug 2015 05:46:29 -0500

This 0.5 fte role will have specific responsibility for the bioinformatic side of a Health Innovation Challenged Fund (HICF) research project investigating the application of Next Generation Sequencing (NGS) technologies to the analysis of Minimal Residual Disease (MRD) in childhood Acute Lymphoblastic Leukaemia (ALL). The successful candidate will be responsible for designing and implementing an analysis pipeline primarily to fit with the clinical need, but with the capacity to answer innovative research questions.

For informal enquiries please contact Anne Walsh via email: anne.walsh@bristol.ac.uk.

Apply at http://www.bris.ac.uk/jobs/find/details.html?nPostingID=3639&nPostingTargetID=13346&option=28&sort=DESC&respnr=1&ID=Q50FK026203F3VBQBV7V77V83&JobNum=ACAD101624&Resultsperpage=10&lg=UK&mask=uobext

NanoPack: visualizing and processing long-read sequencing data

Jit — Tue, 25 Dec 2018 21:20:50 -0600

The NanoPack tools are written in Python3 and released under the GNU GPL3.0 License. The source code can be found at https://github.com/wdecoster/nanopack, together with links to separate scripts and their documentation. The scripts are compatible with Linux, Mac OS and the MS Windows 10 subsystem for Linux and are available as a graphical user interface, a web service at http://nanoplot.bioinf.be and command line tools.

Address of the bookmark: https://github.com/wdecoster/nanopack

RA Bioinformatics at IISR

Mon, 13 Jul 2015 02:12:10 -0500

Bioinformatics Research Associate at Indian Institute of Spice Research

Pay Scale: Rs. 40,000/-per month +HRA (as admissible) for Ph.D. holders and Rs. 38,000/-p.m. + HRA (as admissible) for Master degree holder

Qualifications: a)Essential :

Ph.D.in Biotechnology/ Molecular B iology/ Genetics & Plant Breeding/ Bioinformatics ( Should have the degree in life sciences at gra duate level) OR Post - Graduation in Biotechnology/ Molecular Biology/ Bioinformati cs/Genetics & Plant Breeding

or equivalent with at least two years of research experience and 60% marks. ( should have a degree in life sciences at graduate level)

b) Desirable :

1. Working experience in plant molecular biology

2. Knowledge of Computational Genomics/Proteomics/ Bioinformatics

3. Working knowledge on Computer programming

Walk-in Interview will be held at The Indian Institute of Spices Research, Marikunnu P.O., Kozikode-673012, Kerala on 28/7/2015 at 10.00 AM.

For more details: http://www.spices.res.in/pdf/Mining%20and%20Validation%20Website.pdf

Kevler: Reference-free variant discovery in large eukaryotic genomes

Jit — Tue, 28 Jan 2020 03:21:53 -0600

Welcome to kevlar, software for predicting de novo genetic variants without mapping reads to a reference genome! kevlar's k-mer abundance based method calls single nucleotide variants (SNVs), multinucleotide variants (MNVs), insertion/deletion variants (indels), and structural variants (SVs) simultaneously with a single simple model.

More at https://kevlar.readthedocs.io/en/latest/

https://www.cell.com/iscience/pdf/S2589-0042(19)30259-7.pdf

Address of the bookmark: https://github.com/kevlar-dev/kevlar

Bioinformatics Project Assistant at Vector Control Research Centre (VCRC), Puducherry.

Sun, 19 Jul 2015 19:22:07 -0500

Applications are invited upto 27.07.2015 for filling up of one post of Project Assistant (UNRESERVED) to work under ICMR funded Non-Institutional adhoc project entitled “Biomedical Informatics centre’s of ICMR” at Vector Control Research Centre (VCRC), Puducherry.

Desirable qualification: M.Sc (Life Sciences) with Bioinformatics knowledge and hands on molecular biology tools.

Age: Not exceeding 30 years on the last date of receipt of application

Job work: Molecular modelling studies, Database curation, Metagenomic studies on Dengue virus

Advertisement: http://vcrc.res.in/writereaddata/BIPrj15.pdf

Luigi: a Python package that helps you build complex pipelines of batch jobs.

Neel — Thu, 24 Jun 2021 05:43:31 -0500

Luigi is a Python (3.6, 3.7, 3.8, 3.9 tested) package that helps you build complex pipelines of batch jobs. It handles dependency resolution, workflow management, visualization, handling failures, command line integration, and much more.

Run pip install luigi to install the latest stable version from PyPI. Documentation for the latest release is hosted on readthedocs.

Run pip install luigi[toml] to install Luigi with TOML-based configs support.

Address of the bookmark: https://github.com/spotify/luigi

Bioinformatics Scientist at NIN

Sat, 25 Jul 2015 22:07:49 -0500

No.NIN/PERS/Sch-88/2015-16/

WALK-IN-INTERVIEW (EMPLOYMENT NOTIFICATION)

Eligible candidates are invited to apply for the following post on the ad hoc research project entitled “Biomedical Informatics Centre’s of ICMR” - funded by ICMR at this Institute. The Applications will be received from the individuals on 31st July, 2015 between 9:30 A.M. and 10:30 A.M. at Conference Hall, NIN, Tarnaka, Hyderabad.

Late applications will not be entertained after 10:30 A.M. at any circumstances.

The Candidates may download the Application Form from NIN website: www.ninindia.org

Selection Procedure: Written test and Interview will be conducted to the eligible candidates, if the large numbers of candidates are found to be eligible in the screening. If the lesser number of candidates are found to be eligible in the screening, interview will be conducted only to the short listed candidates for final selection. The names of the shortlisted candidates will be displayed on the Notice Board, which is kept in front of the Conference Hall by 11:30 A.M.

Date of Written Test / Interview: 31st July, 2015. The essential qualification, experience, consolidated Pay and service tenure are as under:

1. Scientist-II (no. of vacancies -1 No.) (UR)

Essential Qualifications :

(i) First Class Master’s Degree in Bio-informatics/ Life Sciences form a recognized University with 4 years R&D experience in the biomedical informatics subject. (or)

(ii) 2nd Class M.Sc./ M.Tech. in Bio-informatics + Ph.D. in the relevant subject from recognized University with 4 years research experience in the biomedical informatics subject.

Age limit : Not exceeding 40 years. Cons.

Pay : Rs.45,954/- p.m. plus 30% HRA p.m. (fixed) without any other allowances.

Tenure : Initially upto 29th February, 2016 and extendable for three more years based on the performance of the candidate and funds position.

Note: Age relaxation will be given to the deserving Candidates. The short listed candidates should bring all original certificates of educational qualification (from SSC onwards), experience, SC/ST/OBC Community Certificate / PH Certificates along with a pass port size photograph and set of Photo copies duly attested for attending the Written Test/Interview. The persons belonging to Other Backward Category should bring the latest O.B.C. (Non-creamy layer) Certificate issued by the respective Tahsildar/ MRO specifically issued for the purpose of applying for Central Government Post. No TA/DA will be paid for attending the Written Test /Interview.

GENERAL CONDITIONS: The conditions of employment will be the same as are for the project staff on contract basis. The candidates have no right to claim for any regular employment at this Institute. The Director In-charge & Appointing Authority has the right to accept / reject any application without assigning any reason/s and no correspondence in this matter will be entertained.

More at http://ninindia.org/31July2015.pdf