BOL: Related items

Bioinformatics Faculty at UNIVERSITY OF HYDERABAD

Wed, 14 Oct 2015 22:53:44 -0500

UNIVERSITY OF HYDERABAD

(A Central University established by an Act of Parliament)

Prof. C.R.Rao Road, P.O. Central University Campus, Gachibowli,

Hyderabad - 500 046

Advt.No. UH/HR/Rectt-2015/02 dt. 12.10.2015

The University invites applications from the Indian citizens for the following positions:

Professor / Associate Professor / Assistant Professor :

Biotechnology & Bioinformatics

Last date : 16th November 2015

More Info : http://www.uohyd.ac.in/images/recruitment/advt-121015.pdf

NextDenovo: string graph-based de novo assembler for TGS long reads

Jit — Sun, 05 Jan 2020 04:08:29 -0600

NextDenovo is a string graph-based de novo assembler for TGS long reads. It uses a "correct-then-assemble" strategy similar to canu, but requires significantly less computing resources and storages. After assembly, the per-base error rate is about 97-98%, to further improve single base accuracy, please use NextPolish.

NextDenovo contains two core modules: NextCorrect and NextGraph. NextCorrect can be used to correct TGS long reads with approximately 15% sequencing errors, and NextGraph can be used to construct a string graph with corrected reads. It also contains a modified version of minimap2 for adapting input and output and producing more sensitive and accurate dovetail overlaps, and some useful utilities (see here for more details).

Address of the bookmark: https://github.com/Nextomics/NextDenovo

SRF/JRF Biotechnology NRCPB - Delhi, Delhi

Fri, 13 Nov 2015 02:52:11 -0600

SRF/JRF job position in National Research Centre on Plant Biotechnology (NRCPB)

JRF /1

Qualification : Master’s Degree in Biotechnology / life sciences with four years Bachelor’s Degree (or) Master’s Degree in Biotechnology / life sciences with NET qualification with 1st Division or 60% marks or equivalent overall grade point average . Non NET/ Master’s degree with three years Bachelor’s degree as per DST/DBT norms. Desirable: Working Experience in Molecular Biology Techniques, genome sequence analysis Bioinformatics

Emoluments : Rs.25000

SRF

Qualification : Master’s degree in Biotechnology/Bioinformatics/Life Science with 1st division or 60% marks or equivalent overall grade point average with 4 year of Bachelor’s degree or 5 years integrated Masters degree. Desirable: Working experience in Bioinformatics, genomic analysis

Emoluments : Rs.25000/

Age Limit: 35 years

Walk-in-interview will be held on 20th November 2015 at 10 AM at NRCPB, LBS Building, Pusa Campus, and New Delhi-110012

More at http://www.nrcpb.org/sites/default/files/Adverdisement_0.pdf

Deepbinner: a signal-level demultiplexer for Oxford Nanopore reads

Jit — Mon, 10 Feb 2020 02:45:53 -0600

Deepbinner is a tool for demultiplexing barcoded Oxford Nanopore sequencing reads. It does this with a deep convolutional neural network classifier, using many of the architectural advances that have proven successful in image classification. Unlike other demultiplexers (e.g. Albacore and Porechop), Deepbinner identifies barcodes from the raw signal (a.k.a. squiggle) which gives it greater sensitivity and fewer unclassified reads.

Address of the bookmark: https://github.com/rrwick/Deepbinner

Teaching Careers 2015 at Uttaranchal College of Science & Technology

Mon, 02 Nov 2015 04:00:26 -0600

Teaching, Non-teaching Careers 2015
Uttaranchal College of Science & Technology - Dehra Dun, Uttarakhand
Teaching, Non-teaching Careers 2015 at Uttaranchal College of Science and Technology, Dehradun

Below mentioned teaching and non-teaching job vacancies are to be recruited.

Assistant Professors job vacancies in the disciplines of:
Biotechnology
Bioinformatics

Eligibility:
Masters Degree in the Discipline along with Ph.D

How to apply:
Candidates who possess requisite eligibility criteria for all the above mentioned positions required to apply on or before 10 days from the date of vacancy notification.

Candidates required to send copies of all the documents along with application

Contact details:
Uttaranchal College of Science & Technology
Nagal Hatnala, P.O. Kulhan Sahastradhara Road,
Dehradun-248001, Uttarakhand, India

More details can be had at:
Dehradun Classifieds e-paper dated 01.11.2015 at page number 40-41

About Employer

Uttaranchal College of Science and Technology, Dehradun, Uttarakhand is affiliated to HNB Garhwal University, Srinagar, Uttarakhand

Employer: Uttaranchal College of Science & Technology
Address: Uttaranchal College of Science & Technology Nagal Hatnala, P.O. Kulhan Sahastradhara Road, Dehradun-248001, Uttarakhand, India
Email: info@ucstdoon.com
URL: http://www.ucstdoon.com
Phone: 0135-2607011, 607413, 3254785, 09719146701

SHAMAN: a user-friendly website for metataxonomic analysis from raw reads to statistical analysis

BioStar — Mon, 17 Aug 2020 05:21:09 -0500

SHAMAN is a shiny application for differential analysis of metagenomic data (16S, 18S, 23S, 28S, ITS and WGS) including bioinformatics treatment of raw reads for targeted metagenomics, statistical analysis and results visualization with a large variety of plots (barplot, boxplot, heatmap, …).
The bioinformatics treatment is based on Vsearch [Rognes 2016] which showed to be both accurate and fast [Wescott 2015].The statistical analysis is based on DESeq2 R package [Anders and Huber 2010] which robustly identifies the differential abundant features as suggested in [McMurdie and Holmes 2014] and [Jonsson2016]. SHAMAN robustly identifies the differential abundant genera with the Generalized Linear Model implemented in DESeq2 [Love 2014].
SHAMAN is compatible with standard formats for metagenomic analysis (.csv, .tsv, .biom) and figures can be downloaded in several formats. A presentation about SHAMAN is available here and a poster here.

More at https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-03666-4

Address of the bookmark: https://github.com/aghozlane/shaman

Project Assistant II Jobs opportunity in National Chemical Laboratory (NCL) on temporary basis

Fri, 06 Nov 2015 01:36:16 -0600

No. Bio/NCIM/3

Project Assistant II Jobs opportunity in National Chemical Laboratory (NCL) on temporary basis

Project Code No. : GAP312626

Title of the Project : Microbial ecology and distribution of geochemical cycling genes in an hot spring ecosystem

No. of Post : 01

Qualifications : M.Sc./B.Tech/M.Tech in Computational biology/ Bioinformatics from recognized university with minimum 60 % marks (aggregate)

Desirable : Good knowledge of computational skills, Linux (command line and GUI) and Unix; Perl / Python / R /C-programming. Practical knowledge of analysis of Next generation sequence datasets (amplicon sequencing, whole metagenome, and complete genome sequencing) with reference to microbes. Analysis and statistical validation of NGS data generated from different chemistry platforms. Some wet-lab experience in microbial system would be an added advantage as project involves some travel.

Emoluments : Rs. 16,000/-

Age Limit : 28 years
How to apply

The application with the above information duly signed together with photo-copies of relevant certificates/testimonials should be addressed to : The Head, NCIM Resource Centre (Attn Dr. M.S. DHARNE), National Chemical Laboratory, Pune 411 008, so as to reach on or before 16th November 2015.

More at http://www.ncl-india.org/files/JoinUs/JobVacancies/TemporaryJobs.aspx?menuid=ql6&childmenustripid=divSubQL6

FastProNGS: fast preprocessing of next-generation sequencing reads

Rahul Nayak — Sat, 26 Dec 2020 08:35:21 -0600

FastProNGS to integrate the quality control process with automatic adapter removal. Parallel processing was implemented to speed up the process by allocating multiple threads. Compared with similar up-to-date preprocessing tools, FastProNGS is by far the fastest.

Address of the bookmark: https://github.com/Megagenomics/FastProNGS

Postdoctoral positions are available at inStem

Tue, 24 Nov 2015 23:24:28 -0600

A position for a Postdoctoral fellow is available in the area of bioinformatics and genomics. The Institute for Stem Cell Biology and Regenerative Medicine (inStem) is a highly collaborative environment and we are seeking an individual who can interface with both wet and dry lab scientists to use profiling technologies to advance our understanding of tissue regeneration and repair. Consequently, the selected candidate for this position can expect world-class training in integrating the fields of cell biology, molecular biology, animal models, and genomics/proteomics.

We are seeking an individual with expertise in analyzing next generation sequencing data, mutation calling in exome seq data, network inference, data integration, and modeling. Competitive candidates would also have programming experience in scripting languages with perl, C, C++, and R programming. This position requires a PhD in Computational Biology, Bioinformatics, Biostatistics or related fields, and evidence of scientific productivity through publications in international journals. Motivation to gain an in-depth understanding of biological phenomena is required! Applications should include a current CV and names of at least three references. Application packages and inquiries regarding this position can be sent to Dr. Dasaradhi Palakodeti ( dasaradhip@instem.res.in ) or Dr. Colin Jamora ( colinj@instem.res.in). Screening of applications will commence immediately and the position will remain open until filled.

More at https://www.instem.res.in/open-positions

HairSplitter: assembling long reads in an unknown number of haplotypes

BioStar — Wed, 07 Dec 2022 00:13:40 -0600

Pros and cons of HairSplitter Limitations of HairSplitter:

Not very fast: it re-polishes the whole assembly

Limited in the number of haplotypes

Strengths of HairSplitter:

Very modular, can be used with any assembler

Naive: makes no assumption on ploidy, parameter-free

Safe: won’t artificially duplicate contigs

HairSplitter splits collapsed assemblies from “draft” assemblies obtained by any means

HairSplitter can recover haplotypes and distinguish repeated elements

Only needs sequencing reads, potentially error-prone

HairSplitter splits collapsed assemblies from “draft” assemblies obtained by any means

HairSplitter can recover haplotypes and distinguish repeated elements

Only needs sequencing reads, potentially error-prone

Not really available yet (github.com/RolandFaure/HairSplitter)

https://hal.archives-ouvertes.fr/hal-03864075/file/RolandFaure_presentation_SeqBIM_2022.pdf

Address of the bookmark: https://hal.archives-ouvertes.fr/hal-03817928/document