BOL: Related items

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

20th International BioInformatics Workshop on Virus Evolution and Molecular Epidemiology (VEME)

Mon, 12 Jan 2015 01:39:45 -0600

20th International BioInformatics Workshop on Virus Evolution and Molecular Epidemiology (VEME)
9 - 14 August 2015 St. Augustine, Trinidad and Tobago

Organiser: Christine Carrington (University of the West Indies - UWI, St. Augustine, Trinidad and Tobago)
Co-organisers: Anne-Mieke Vandamme, Philippe Lemey (Katholieke Universiteit Leuven, Belgium), Marco Salemi, Mattia Prosperi (University of Florida, Gainesville, USA) and Karen E. Nelson (J. Craig Venter Institute, Rockville, USA)

Requests for information directly to:
Christine Carrington
Department of Preclinical Sciences
Faculty of Medical Sciences
University of the West Indies (UWI)
St. Augustine
Trinidad and Tobago
Telephone: +1-868-6452640 ext. 5009, +1-868-6848803
Fax: +1-868-6621873
E-mail: veme2015@sta.uwi.edu

Deadline for receipt of applications by local organiser: 15 March 2015
CALL FOR APPLICATIONS NOW OPEN
http://www.icgeb.org/course-application-trinidad-and-tobago-2015.html

http://rega.kuleuven.be/cev/veme-workshop/2015

TULIP - The Uncorrected Long read Itegration Pipeline

Jit — Thu, 23 Nov 2017 09:30:01 -0600

#Running TULIP (The Uncorrected Long-read Integration Process), version 0.4 late 2016 (European eel)

TULIP currently consists of to Perl scripts, tulipseed.perl and tulipbulb.perl. These are very much intended as prototypes, and additional components and/or implementations are likely to follow.
Tulipseed takes as input alignments files of long reads to sparse short seeds, and outputs a graph and scaffold structures. Tulipbulb adds long read sequencing data to these.

https://github.com/Generade-nl/TULIP

Address of the bookmark: https://github.com/Generade-nl/TULIP

WuXi has acquired NextCODE Health

Pranjali Yadav — Mon, 19 Jan 2015 08:17:35 -0600

Shanghai, China-headquartered pharmatech company WuXi (NYSE: WX) has acquired NextCODE Health, a genomic analysis and bioinformatics company based in the USA.

The acquisition was made for $65 million in cash, and WuXi plans to merge its genome center with NextCODE Health to form a new company, WuXi NextCODE Genomics. The business will be headquartered in Shanghai and have operations in Cambridge, Massachusetts, and Reykjavik, Iceland.

With the huge unmet medical needs in diseases with a genetic component and the rapid advances in genomics and bioinformatics, now is the right time for WuXi to make a strategic investment in this field, and NextCODE is the right partner. This new venture of WuXi NextCODE Genomics will create important new genomic and bioinformatic products and services to help make personalized treatment and medicine a reality. It will also enable doctors to provide better treatments to patients.

YAMP: Yet Another Metagenomic Pipeline

BioStar — Sat, 06 Jul 2024 04:26:00 -0500

YAMP is constructed on Nextflow, a framework based on the dataflow programming model, which allows writing workflows that are highly parallel, easily portable (including on distributed systems), and very flexible and customisable, characteristics which have been inherited by YAMP. New modules can be added easily and the existing ones can be customised -- even though we have already provided default parameters deriving from our own experience.

Address of the bookmark: https://github.com/alesssia/YAMP

RA Bioinformatics at CIBA

Fri, 13 Feb 2015 11:23:18 -0600

Recruitment The following posts are to be filled purely on temporary basis under CIBA Component of “Centre for Agricultural Bioinformatics (CABin)” project at this Institute.

Posts Research Associate

Date & Time of Interview 18th Feb 2015 at 10.00 a.m.

Project Name “Centre for Agricultural Bioinformatics (CABin)”

Duration 12th Plan (2012-2017) / co-terminus with the project 12th Plan (2012-2017) / co-terminus with the project

Essential Qualification Ph.d / M.Sc./ M.Phil (Bioinformatics) With 1st division or 60% marks or equivalent overall grade point average with at least two years of research experience in the relevant subject.

Technician

B.Tech. or Master degree in computer science/Computer Engineering /MCA or equivalent. Desirable qualification: Experience in Java/ C++/ PHP/ PERL/ Python etc. based application development using Linux, Apache and MySQL/Oracle.

Emoluments Rs.24000/- p.m. + 30% HRA for Ph.D holders / Rs.23000/- p.m. + 30% HRA for Master Degree holders A consolidated pay Rs.25000/- per month.

Age Limit Maximum 40 years for men and 45 years for women as on date of interview.

Age limits are relaxable for SC / ST / OBC candidates as per rules.

Maximum 40 years for men and 45 years for women as on date of interview.

Age limits are relaxable for SC / ST / OBC candidates as per rules.

Eligible Candidates may send their Curriculum Vitae along with the contact numbers to ashok@ciba.res.in on or before 13-02-2015.

Candidates selected after initial screening will be called for interview.

Advertisement: www.ciba.res.in/attachments/jobs/CABin-3006.pdf

Unicycler: Hybrid assembly pipeline for bacterial genomes

Jit — Fri, 10 Nov 2017 03:58:27 -0600

Unicycler is an assembly pipeline for bacterial genomes. It can assemble Illumina-only read sets where it functions as a SPAdes-optimiser. It can also assembly long-read-only sets (PacBio or Nanopore) where it runs a miniasm+Racon pipeline. For the best possible assemblies, give it both Illumina reads and long reads, and it will conduct a hybrid assembly.

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

Postdoctoral Researcher at Department of Biotechnology, Catholic University of Daegu, Kyungsan, Kyungbuk, South Korea.

Thu, 29 Jan 2015 12:11:16 -0600

Applications are invited from Indian nationals for a Post Doctoral position at Molecular Medical Laboratory, Department of Biotechnology, Catholic University of Daegu, Kyungsan, Kyungbuk, South Korea.

Qualification required: PhD in Life Sciences/ Molecular Biology/ Bioinformatics or related discipline.

Desirable Qualification:

1. Candidates having experience in molecular biology techniques and must be well versed with bioinformatics tool or expert in relevant fields will be preferred.
2. The candidate should have good communication skill, knowledge about designing experiments and analyzing data.
3. Sense of initiative, autonomy, organization and thoroughness, good relation qualities.
Remuneration: 2000USD per month.

Last date of submitting the complete applications furnishing Bio-data is 10th February, 2015.

Interested candidates should send their resume including all personal as well as academic details to the principal investigator Prof Seung-Won Park (email:microsw@cu.ac.kr)

The shortlisted candidates will be intimated within February 2015.

3d-dna: 3D de novo assembly (3D DNA) pipeline

Jit — Thu, 28 Dec 2017 10:09:37 -0600

This code is designed to enable anyone to reproduce the Hs2-HiC and the AaegL4 genomes reported in: Dudchenko et al., De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science, 2017.

Unless otherwise noted, all terminology below is consistent with this paper, and all references to figures and tables in this readme refer to this paper. Specifically, some of the terminology used below is outlined in Figure S2. The assembly procedure is described in detail in the Supporting Online Materials, specifically in the section labelled “Pipeline description”.

In addition, the pipeline uses tools and methods from Juicer (Durand & Shamim et al., Cell Systems, 2016) and Juicebox (Durand & Robinson et al., Cell Systems, 2016), as well as additional dependencies noted below.

Feel free to post your questions and comments at: http://www.aidenlab.org/forum.html

http://aidenlab.org/documentation.html

Address of the bookmark: https://github.com/theaidenlab/3d-dna

Research Associate NBFGR - Lucknow, Uttar Pradesh

Thu, 28 May 2015 19:37:22 -0500

NBFGR, Lucknow is recruiting Bioinformatics experts for the post of Research Associate

Name of Position : Research Associate
No of Post : One
Desired candidate Profile : Candidate should be PhD in Bioinformatics or equivalent or Post-Graduation Bioinformatics with 1st division or 60% marks. Preference will be given to candidates having experience in server management
Remuneration : Rs 24000/- pm + HRA for PhD holders
Age requirement- 40 years (5 years relaxation for SC/ST/women candidates and 3 years for OBC candidates) as on date of interview.

How to apply- Interested candidates can walk -in-interview on 30.05.2015 at 10:00 hrs at National Bureau of Fish Genetic Resources, Lucknow.

Ref- http://www.nbfgr.res.in/PDF/News%20&%20Events/Walk%20in%20interview%20on%2030.05.2015.pdf