BOL: Related items

Bioinformatics Faculty at University of Pune

Fri, 13 Nov 2015 03:06:00 -0600

SAVITRIBAI PHULE PUNE UNIVERSITY
(Formerly University of Pune)
(APPOINTMENT OF TEACHING POSTS)

Accompaniment to the Advertisement No. 52 dated 10.11.2015 for various Teaching Positions purely on contract basis for a maximum period of five years in the various Departments/Centre of the University.

Last date for receipt of application in the University Office is 04.12.2015.

Associate Professor

Environmental Science

Institute of Bioinformatics & Biotechnology (IBB)

Microbiology

Assistant Professor

Biotechnology

Institute of Bioinformatics & Biotechnology (IBB)

Microbiology

More Info : http://collegecirculars.unipune.ac.in/sites/documents/Job%20Openings/advt-no-52-dt-10-11-2015-contract-positions.pdf

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.

Postdoctoral positions are available at the Faryabi Lab

Sun, 11 Oct 2015 03:36:18 -0500

Postdoctoral positions are available at the Faryabi Lab located in the Department of Pathology and the Center for Personalized Diagnostics at the University of Pennsylvania.

A qualified candidate will be strongly motivated individual with following qualifications: a Ph.D. in computational sciences, engineering, physics, bioinformatics, or related field. Ability to program in Python/Perl and R in Unix environment, knowledge of C++, Java, and SQL is a plus. Demonstrated applied bioinformatics/computational proficiency as evidenced by relevant publications in peer-reviewed journals. Experience with cancer genomics is a plus.

The primary research focus of the Faryabi Lab is on developing novel computational methods to study mechanisms involved in genome instability and elucidate their roles in tumorigenesis. In addition the position provides collaborative opportunities with both basic and translational scientists across the Perelman School of Medicine, one of the top 5 medical research universities in the nation.
. a Ph.D. degree in either physical or computational sciences
. solid programming skills ( Python/Perl, Java, C/C++, R, SQL)
. computational genomics experience ( high throughput sequence analysis)
. excellent spoken and written communication and interaction skills
. publications in English in relevant areas of research in peer-reviewed journals.
. Previous experience or interest in data visualization design is a plus.

More at
University of Pennsylvania
Pathology and Laboratory Medicine
Robert B. Faryabi
faryabiPenn@gmail.com
http://faryabib.github.io/
How To Apply: email CV and contacts of 3 references to faryabiPenn@gmail.com

List of bioinformatics workflow management tools !

Rahul Nayak — Sat, 20 Mar 2021 00:15:25 -0500

Here are list of Workflow Managers

BigDataScript – A cross-system scripting language for working with big data pipelines in computer systems of different sizes and capabilities. [ paper-2014 | web ]
Bpipe – A small language for defining pipeline stages and linking them together to make pipelines. [ web ]
Common Workflow Language – a specification for describing analysis workflows and tools that are portable and scalable across a variety of software and hardware environments, from workstations to cluster, cloud, and high performance computing (HPC) environments. [ web ]
Cromwell – A Workflow Management System geared towards scientific workflows. [ web ]
Galaxy – a popular open-source, web-based platform for data intensive biomedical research. Has several features, from data analysis to workflow management to visualization tools. [ paper-2018 | web ]
Nextflow (recommended) – A fluent DSL modelled around the UNIX pipe concept, that simplifies writing parallel and scalable pipelines in a portable manner. [ paper-2018 | web ]
Ruffus – Computation Pipeline library for python widely used in science and bioinformatics. [ paper-2010 | web ]
SeqWare – Hadoop Oozie-based workflow system focused on genomics data analysis in cloud environments. [ paper-2010 | web ]
Snakemake – A workflow management system in Python that aims to reduce the complexity of creating workflows by providing a fast and comfortable execution environment. [ paper-2018 | web ]
Workflow Descriptor Language – Workflow standard developed by the Broad. [ web ]

Research Associates/Research Fellow - School of Agricultural Biotechnology (Last Date 17-11-2015 and Interview on 26-11-2015 at 11.00 AM)

Fri, 13 Nov 2015 02:46:59 -0600

PAU Recruitment November 2015, Punjab

Job notification in Punjab Agricultural University (PAU) for research Associate/ Research Fellow posts for different projects. Eligible candidates may apply in prescribed application format on or before 17-11-2015 from 09:00 am to 05:00 pm.

Vacancies:
Research Associate/ Research Fellow-03
Qualification:
Candidates should possess B.Sc. with minimum 50% marks, M.Sc. in Bioinformatics/ Biotechnology/ Genetics/ Plant Breeding/ Plant Breeding & Genetics/ Plant Breeding, Genetics & Biotechnology/ Microbiology/ Biochemistry/ Botany with 65% marks.
Selection Process:
Selection will be based on interview.
How to Apply:
Eligible candidates may send their applications along with attested copies of certificates, fee to the Director, School of Agricultural Biotechnology, PAU, Ludhiana on or before 17-11-2015 from 09:00 am to 05:00 pm
Last Date:
17-11-2015

More at http://web.pau.edu/content/banner/1349.pdf

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

JRF Bioinformatics

Mon, 02 Nov 2015 03:24:50 -0600

JRF Bioinformatics

Eligibility : ME/M.Tech, MSc(Bio-Chemistry, Bio-Informatics, Bio-Tech, Microbiology), BE/B.Tech

Location : Gandhinagar

Last Date : 05 Nov 2015

Hiring Process : Face to Face Interview

Junior Research Fellow (JRF) Job vacancies in Gujarat State Biotechnology Mission (GSBTM)

Project : “Establishing a network in computational and system biology”

No. of Post : 01

Qualification : MSc. /M.Tech. /B.E. /B.Tech. in Biotechnology/Bioinformatics /Life Sciences /Microbiology /Biochemistry /Genetics from recognized University. Preference would be given to the candidates having NET/GATE.

Fellowship : Rs. 12,000 + 20% HRA
How to apply

Applications should be filled Online. The last date for submission of application is 5th November, 2015.

More at http://btm.gujarat.gov.in/btm/recruitment2.htm

ngs-bits - Short-read sequencing tools

Neel — Thu, 16 Jan 2020 23:14:00 -0600

Binaries of ngs-bits are available via Bioconda. Alternatively, ngs-bits can be built from sources:

Binaries for Linux/macOS
From sources for Linux/macOS
From sources for Windows

Address of the bookmark: https://github.com/imgag/ngs-bits

Project Assistant-II job vacancies in National Institute of Oceanography (NIO Goa)

Fri, 06 Nov 2015 01:33:22 -0600

Vacancy no : GAP0423/1509-15

Project Assistant-II job vacancies in National Institute of Oceanography (NIO Goa)

Project Title and Code : Biotechnology Information System. -- GAP0423

Qualification : M.Sc Bioinformatics / Zoology / Botany / Environmental Science. Desirable : Basic understanding of biodiversity concept is desirable

No. of Post : 01

Age : 28 Years

Place of Posting : Goa

Consolidated Stipend Per Month : Rs.16000/-

Job Requirement : Collection and handling of biodiversity data as assigned by the scientists and working with in-house biodiversity data management applications and software
How to apply

Candidates satisfying requirements may attend the Walk-in-interview on 12.11.2015, 10.00 AM at NIO Dona Paula, Goa-403004 along with their bio-data, attested copies of certificates & mark lists in proof of qualification (SSC onwards), age, experience and testimonials. Candidates should bring a photo identity proof at the time of registration

More at http://www.nio.org/index/option/com_vacgoa/task/show/title/Goa/tid/6/sid/28/thid/64

SRF/JRF Bioinformatics at National Bureau of Animal Genetic Resources

Thu, 26 Nov 2015 01:54:07 -0600

National Bureau of Animal Genetic Resources

SRF Job vacancies in National Bureau of Animal Genetic Resources (NBAGR) on contractual basis

No. of Posts : 03

Qualifications : Master degree in any one of discipline/ Subjects Biotechnology/Bioinformatics/Life Sciences/ Computer Applications with 4 years/5 years of Bachelor’s degree. Candidates having post graduate degree in above mentioned subjects with 3 years Bachelor’s degree should be NET qualified.

Note : i. The Ph.D. Degree holders are eligible for the posts. ii. The Master’s degree holders with the integrated degrees like B.Tech. & M. Tech. (5 years) are eligible. iii. Graduates with three years Bachelor’s degree, who have acquired professional Master’s degree (3 years) like M.Sc. (Ag.), Masters in Computer Applications, M. Tech., etc., are eligible.

Desirable : The candidates should have zeal to work in R environment and NGS data analysis

Emolument : Rs. 28,000/-

Age Limit : 35 year for Men and 40 years for Women in case of SRF on the date of Interview.
How to apply

Walk-in-Interview is proposed to be held at National Bureau of Animal Genetic Resources, Karnal (Haryana)-132 001 at 10:30 AM on 02.12.2015. Interested candidates may attend Walk-in-Interview at 10:30 AM on 02.12.2015 alongwith original certificates and typed bio-data with one set of attested copies of each their certificates with passport size photograph.