BOL: Related items

2 positions on the evolutionary analysis of biological sequences in Montpellier - France

Mon, 28 Sep 2015 08:25:48 -0500

The Methods and Algorithms for Bioinformatics (MAB) team at the LIRMM (computer science, robotics and microelectronics laboratory at the CNRS & University of Montpellier, France) is looking for talented individuals to fill two postdoctoral positions. We are seeking candidates with a strong background in computational evolutionary biology. The positions will start by the end of 2015.

The first of the positions (duration: 18-24 months), associated with the European VIROGENESIS project (http://www.kuleuven.be/english/research/EU/p/horizon2020/sc/sc1/Virogenesis), concerns the evolutionary analysis of viral sequences. Topics include -- but are not limited to -- phylogenetic classification of metagenomic reads and the recombination history of viruses.

The second position (duration: 1 year), associated with the Institute for Computational Biology (IBC, http://www.ibc-montpellier.fr), concerns evolutionary analyses of large-scale genomic data -- including the inference of very large phylogenies, gene/species tree reconciliation, comparative genomics, phylogenetic network inference and verification, phylogeography, the use of phylogenies to study the evolution of characters.

A one thousand year old city, Montpellier is a thriving research community with a multitude of biology and biomedical research centers. It is the fastest growing city in France where approximately one third of the population are students, and a wonderful location for outdoor activities (kite/wind surfing, sailing, river/sea kayaking, hiking and rock climbing). The LIRMM is one of the most visible computer science laboratories in France.

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

Jit — Mon, 20 Aug 2018 04:08:50 -0500

Here is the command to run the tool:

python finisherSC.py destinedFolder mummerPath

If you are running on server computer and would like to use multiple threads, then the following commands can generate 20 threads to run FinisherSC.

python finisherSC.py -par 20 destinedFolder mummerPath

Sometimes, if the names of raw reads and contigs consists of special characters/formats, FinisherSC/MUMmer may not parse them correctly. In that case, you want to have a quick renaming of the names of contigs/reads in contigs.fasta or raw_reads.fasta using the following command.

    perl -pe 's/>[^\$]*$/">Seg" . ++$n ."\n"/ge' raw_reads.fasta > newRaw_reads.fasta
    cp newRaw_reads.fasta raw_reads.fasta
    perl -pe 's/>[^\$]*$/">Seg" . ++$n ."\n"/ge' contigs.fasta > newContigs.fasta
    cp newContigs.fasta contigs.fasta

Address of the bookmark: https://github.com/kakitone/finishingTool

SRF/JRF Bioinformatics at IARI

Sun, 29 Nov 2015 03:00:44 -0600

Agricultural Knowledge Management Unit

ICAR-INDIAN AGRICULTURAL RESEARCH INSTITUTE

L.B.S Building, Pusa Campus,

New Delhi-110012

Walk-in-Interview: 18th December 2015

DBT funded project: Distributed Information Centre under BTISnet (PI: Dr. A.K.Mishra)

Senior Research Fellow Two

Rs 28000/- + HRA

i) Master’s degree in Bioinformatics or Computer Science+ NET qualification and two years research experience, or

ii) M. Tech degree in Bioinformatics or Computer Science /Engineering with two years research experience Efficiency to handle agricultural databases and bioinformatics tool development

#Junior Research Fellow

Rs. 25000/- + HRA

i) Master’s degree in Bioinformatics or Computer Science + NET qualification, or

ii) M. Tech degree in Bioinformatics or Computer Science/Engineering Efficiency to handle agricultural databases and bioinformatics tool development

Traineeship Two

Rs. 8000/- consolidated

M.Sc./M. Tech (Bioinformatics) with 60 % marks from a recognized University

Studentship Four

Rs. 8000/- consolidated

Final year M.Sc./ M.Tech (Bioinformatics) Students from a recognized University

* M. Tech with Four Years Bachelor’s degree followed by Master’s degree

# In case suitable person is not found for SRF position, it may be filled at the JRF level The interview will be held on 18 th December 2015 at 10:00 AM at AKMU, LBS Building, IARI, Pusa Campus, New Delhi-110012. Terms and Conditions:  Maximum age limit is 35 years for all positions. Age relaxation of 5 yrs for SC/ST/OBC and woman candidates will be given.  The above post is purely temporary and is co-terminus with the project. The candidate shall not claim for regular appointment.  No TA/DA will be paid for attending the interview.  Bring self attested copies and originals of all certificates ( class 10th )onwards along with biodata in the attached format, proof of date of birth, one passport size photo, NOC from present employer, if any  Canvassing in any form will disqualify the candidate. 

Reporting time for interview: 9.30-10.00 AM at AKMU, IARI, New Delhi -110 012

www.iari.res.in/files/SRF_JRF_Akkmu-27112015-20151127-124003.pdf

rHAT: a seed-and-extension-based noisy long read alignment tool

Abhimanyu Singh — Sun, 23 Sep 2018 05:12:22 -0500

rHAT is a seed-and-extension-based noisy long read alignment tool. It is suitable for aligning 3rd generation sequencing reads which are in large read length with relatively high error rate, especially Pacbio's Single Molecule Read-time (SMRT) sequencing reads.

Address of the bookmark: https://github.com/dfguan/rHAT

RA Bioinformatics at NIPGR

Tue, 20 Oct 2015 04:11:56 -0500

Applications are invited from suitable candidates for filling up the purely temporary positions of one Research Associate (RA) and one Junior Research Fellow (JRF) in the DBT Part-B Sub-project-1&2 entitled Transcriptome and epigenome diversity analysis during seed development for discovery of molecular markers and gene regulatory mechanism in chickpea of Seed Biology

Research Associate (one post): Emoluments as per DST/DBT norms & as sanctioned in the project
Qualification: Candidates having Ph.D. degree (awarded) in Life Sciences/Molecular Biology/Bioinformatics or related field are eligible to apply.

Junior Research Fellow (one post): Emoluments as per DST/DBT norms & as sanctioned in the project
Qualification: Candidates having M.Sc. degree or equivalent (with minimum 55% marks) in Life Sciences, Biotechnolgy, Bioinformatics, Molecular Biology or any other related field are eligible to apply

Additional Information

Address:
Staff Scientist
National Institute of Plant Genome Research (NIPGR)
Aruna Asaf Ali Marg, P.O. Box NO. 10531,
New Delhi - 110067

States & U.T
State & Union Territories Delhi

How To Apply

Apply Details
Eligible candidates may apply by sending their complete application in the given format. The attested copies of the certificates and proof of research experience (if any) are to be attached with the hard copy of application. The applications should reach at the address given below within 15 days from the date of advertisement.

Web/Notification URL
http://www.nipgr.res.in/careers/vacancie s_latest.php

ClipCrop: a tool for detecting structural variations with single-base resolution using soft-clipping information

BioJoker — Sun, 20 Jan 2019 06:34:36 -0600

ClipCrop for detecting SVs with single-base resolution using soft-clipping information. A soft-clipped sequence is an unmatched fragment in a partially mapped read. To assess the performance of ClipCrop with other SV-detecting tools, we generated various patterns of simulation data – SV lengths, read lengths, and the depth of coverage of short reads – with insertions, deletions, tandem duplications, inversions and single nucleotide alterations in a human chromosome.

Address of the bookmark: https://github.com/shinout/clipcrop

Project Assistant BioInformatics

Mon, 02 Nov 2015 03:23:09 -0600

Project Assistant BioInformatics

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

Location : Pune

Last Date : 16 Nov 2015

Hiring Process : Face to Face Interview

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

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

vt: a variant tool set that discovers short variants from Next Generation Sequencing data.

Jit — Tue, 28 Jan 2020 03:44:43 -0600

vt is a variant tool set that discovers short variants from Next Generation Sequencing data.

https://genome.sph.umich.edu/wiki/Vt

https://github.com/atks/vt

Address of the bookmark: https://genome.sph.umich.edu/wiki/Vt

Pre- or postdoctoral research fellowship in Structural Bioinformatics at Padova

Thu, 05 Nov 2015 22:15:12 -0600

A research fellowship for a software developer is available at the BioComputing UP Laboratory, University of Padova (URL: http://protein.bio.unipd.it/).
A highly motivated and creative candidate is sought to work on structural bioinformatics. Specifically, the project entails the development of novel methods, tools and databases for the analysis of protein structures.

The BioComputing UP Laboratory, headed by Prof. Silvio Tosatto, is a dynamic group of a dozen people working on several aspects of prediction of protein structure & function employing techniques at the intersection between biology, medicine, chemistry, physics & computer science.
Our aim is to integrate the development of novel methods and their application to biologically relevant problems.

We are looking for candidates with a solid Bioinformatics background, programming experience (Python, C++ and/or Java) and good knowledge of molecular biology (protein structure/function). Good knowledge of statistics as well as experience in using database systems (MongoDB, MySQL and/or Postgres) is desirable. Candidates should have a degree with top marks, optionally hold a PhD, and be highly motivated to work on interdisciplinary research. Good knowledge of English, an open-minded spirit, being collaborative and creative are crucial.

The fellowship, which should start as soon as possible, is renewable and initially for one year. It will be commensurate to experience, can be extended depending on performance and may lead to a PhD degree. The successful candidate will be working full-time at the BioComputing UP Laboratory, University of Padova. Travel support for conferences and/or research visits abroad is provided.
To apply, please send your CV, with a motivation letter and brief description of your research background as well as the names of two (or more) references to: biocomp@bio.unipd.it.

Start date: As soon as possible

Duration: 1 year, renewable

Salary on grant: Commesurate to experience

Contact Person (Referent): Silvio Tosatto

Ref. E-Mail: biocomp@bio.unipd.it

Tel: +39 049 827 6269
Fax: +39 049 827 6260

Group Web Page: http://protein.bio.unipd.it/

Filtlong: quality filtering tool for long reads

Radha Agarkar — Wed, 13 May 2020 10:23:55 -0500

Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.

Filtlong builds into a stand-alone executable:

git clone https://github.com/rrwick/Filtlong.git
cd Filtlong
make -j
bin/filtlong -h

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