BOL: Related items

Oxford Nanopore Sequencing, Hybrid Error Correction, and de novo Assembly of a Eukaryotic Genome

Jit — Wed, 29 Nov 2017 05:08:53 -0600

Monitoring the progress of DNA molecules through a membrane pore has been postulated as a method for sequencing DNA for several decades. Recently, a nanopore-based sequencing instrument, the Oxford Nanopore MinION, has become available that we used for sequencing the S. cerevisiae genome. To make use of these data, we developed a novel open-source hybrid error correction algorithm Nanocorr (https://github.com/jgurtowski/nanocorr) specifically for Oxford Nanopore reads, as existing packages were incapable of assembling the long read lengths (5-50kbp) at such high error rate (between ~5 and 40% error). With this new method we were able to perform a hybrid error correction of the nanopore reads using complementary MiSeq data and produce a de novo assembly that is highly contiguous and accurate: the contig N50 length is more than ten-times greater than an Illumina-only assembly (678kb versus 59.9kbp), and has greater than 99.88% consensus identity when compared to the reference. Furthermore, the assembly with the long nanopore reads presents a much more complete representation of the features of the genome and correctly assembles gene cassettes, rRNAs, transposable elements, and other genomic features that were almost entirely absent in the Illumina-only assembly.

Address of the bookmark: http://schatzlab.cshl.edu/data/nanocorr/

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.

Genome assembly stats plotting

Jit — Wed, 28 Feb 2018 03:45:39 -0600

A de novo genome assembly can be summarised b

y a number of metrics, including:

Overall assembly length
Number of scaffolds/contigs
Length of longest scaffold/contig
Scaffold/contig N50 and N90Assembly base composition, in particular percentage GC and percentage Ns
CEGMA completeness
Scaffold/contig length/count distribution

assembly-stats supports two widely used presentations of these values, tabular and cumulative length plots, and introduces an additional circular plot that summarises most commonly used assembly metrics in a single visualisation. Each of these presentations is generated using javascript from a common (JSON) data structure, allowing toggling between alternative views, and each can be applied to a single or multiple assemblies to allow direct comparison of alternate assemblies.

Tabular presentation allows direct comparison of exact values between assemblies, the limitations of this approach lie in the necessary omission of distributions and the challenge of interpreting ratios of values that may vary by several orders of magnitude.

Address of the bookmark: https://github.com/rjchallis/assembly-stats

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

The MARVEL assembler

Jit — Fri, 04 May 2018 19:18:41 -0500

MARVEL consists of a set of tools that facilitate the overlapping, patching, correction and assembly of noisy (not so noisy ones as well) long reads.

The assembly process can be summarized as follows:

overlap
patch reads
overlap (again)
scrubbing
assembly graph construction and touring
optional read correction
fasta file creation

Address of the bookmark: https://github.com/schloi/MARVEL

RA Bioinformatics at IISER

Fri, 06 Feb 2015 04:05:49 -0600

Advertisement: Research Position in Computational Biology in the group of Shree P. Pandey Positions available in the area of NGS data analysis, bioinformatics, plant genomics Project Description: Projects involves high throughput analysis of data mostly generated by massively parallel sequencing (RNA-Seq and small-RNA-Seq), microarrays and related platforms.

We are looking for highly motivated and bright individuals interested in high-throughput cutting-edge data analyses methods in genomics (computational positions). Available positions:

Applications are invited from suitable candidates in both, the Max Planck India Partner Program and the CRP Wheat Program for openings at the levels:

Minimum qualification Salary scale (per month)

Project assistant Bachelor’s / Master’s Rs. 10000 / Rs. 14000

Project fellow (junior data analyst) Masters + research experience Rs. 16000

Research fellow (senior data analyst) Masters + adequate research experience/desirable skill sets Rs. 22000

Research Associated PhD (<1yr) / > 1 yr experience Rs. 28000 / Rs. 32000

Condition to satisfactory performance, availability of funds and requirements of the project, the positions could be available upto a period of ~2 years (or funding of the project).

Essential qualification: MSc/BTech/MTech/PhD (or other suitable qualification) in discipline related to bioinformatics, computational biology, computer application (or equivalent)/ ‘Advance PostGraduate Diploma in Bioinformatics’. Proficiency in one of the programming languages or statistics (proficient in R for example) is compulsory.

Desirable qualification:

1. Programming experiences in at least one low level language such as C/C++ and one scripting language such as Perl/Python/PHP and knowledge of SQL/MySQL.

2. Substantial experience in the linux or other unix environments.

Application process: Applications should contain CV along with brief description (maximum 1 page) of research conducted (highlighting skills and experience) till now. Applications should be sent by email to Shree P. Pandey, Department of Biological Sciences, IISER-Kolkata, Mohanpur Campus, West Bengal within 2 weeks (Feb 19th 2015). E-mail: sppiiserkol@gmail.com, sppandey@iiserkol.ac.in Brief description of the group: We are an interdisciplinary group focusing on small-RNA (miRNA, siRNA) mediated regulation of signaling and defense. Project equally involve bioinformatics and systems biology (specially microarrays and next-generation sequencing (NGS) data analysis and its use), along with plant molecular biology, genetic engineering, field biology, and analytical plant chemistry for understanding response of plants to biotic stresses. For more details visit: http://www.iiserkol.ac.in/~sppandey/

www.iiserkol.ac.in/images/iiserk/advertisements/advertisement_7_spp_feb_2015.pdf

GAPPadder: A Sensitive Approach for Closing Gaps on Draft Genomes with Short Sequence Reads

Jit — Mon, 14 May 2018 05:25:48 -0500

This software is provided ``as is” without warranty of any kind. In no event shall the author be held responsible for any damage resulting from the use of this software. The program package, including source codes, executables, and this documentation, is distributed free of charge. If you use this program in a publication, please cite the following reference:
Chong Chu, Xin Li, and Yufeng Wu. "GAPPadder: A Sensitive Approach for Closing Gaps on Draft Genomes with Short Sequence Reads." bioRxiv (2017): 125534.

Address of the bookmark: https://github.com/Reedwarbler/GAPPadder

RA Bioinformatics at North Eastern Hill University

Sat, 07 Feb 2015 06:06:05 -0600

Bioinformatics Infrastructure Facility, Department of RDAP, NEHU vacancy of Research Associate

Name of the Post: Research Associate
No. of the Post: 01 One
Age Limit: Max. 35 years
Salary: Rs. 22000/- per month plus HRA

Required Job Profile:
Candidate must possess M.Sc. in bioinformatics or biotechnology from recognized university or institute.
Desired Job Profile;
Candidate having Ph.D. or pursuing Ph.D. in the related subject or equivalent published work in reputed peer reviewed journals or advance PG dipoma in bioinformatics course.

How to apply:
Eligible and interested candidates should need to send the bio-data and bring all related documents in original and set of attested copies of the same in the time of interview.

Last date: 16.02.2015
Refer to http://www.nehu.ac.in/Advertisements/BIFTuraAdvt_221214.pdf

Summary
Employer Address: Dr.B.K. Mishra Coordinator BIF, RDAP Department, North Eastern Hill University, Tura Campus, Tura, Meghalaya
Email: drbkm1972@yahoo.co.in;birendramishra14@gmail.com
URL: http://www.nehu.ac.in/Advertisements/BIFTuraAdvt_221214.pdf
Phone: 03651-223107
Required Skills: not mentioned / required for this post
Required Experience: not mentioned / required for this job post
Required Education: M.Sc. in bioinformatics or biotechnology from recognized university or institute.
Job Location: Tura, Meghalaya, India

CGView - Circular Genome Viewer

Rahul Nayak — Wed, 20 Jun 2018 10:15:57 -0500

CGView is a Java package for generating high quality, zoomable maps of circular genomes. Its primary purpose is to serve as a component of sequence annotation pipelines, as a means of generating visual output suitable for the web. Feature information and rendering options are supplied to the program using an XML file, a tab delimited file, or an NCBI ptt file. CGView converts the input into a graphical map (PNG, JPG, or Scalable Vector Graphics format), complete with labels, a title, legends, and footnotes. In addition to the default full view map, the program can generate a series of hyperlinked maps showing expanded views. The linked maps can be explored using any web browser, allowing rapid genome browsing, and facilitating data sharing. The feature labels in maps can be hyperlinked to external resources, allowing CGView maps to be integrated with existing web site content or databases. For examples of the various output types, see the CGView gallery. http://wishart.biology.ualberta.ca/cgview/gallery.html http://stothard.afns.ualberta.ca/downloads/CCT/index.html https://www.gview.ca/wiki/GView/WebHome https://server.gview.ca/ http://stothard.afns.ualberta.ca/cgview_server/ Paper https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bbx081/4037458

Address of the bookmark: http://wishart.biology.ualberta.ca/cgview/

Pacman

Rahul Nayak — Mon, 16 Feb 2015 12:15:17 -0600

The pacman package is an R package management tool that combines the functionality of base library related functions into intuitively named functions. This package is ideally added to .Rprofile to increase workflow by reducing time recalling obscurely named functions, reducing code and integrating functionality of base functions to simultaneously perform multiple actions.

Function names in the pacman package follow the format of p_xxx where ‘xxx’ is the task the function performs. For instance the p_load function allows the user to load one or more packages as a more generic substitute for the library or require functions and if the package isn’t available locally it will install it for you.

Installation

To download the development version of pacman:

Download the zip ball or tar ball, decompress and run R CMD INSTALL on it, or use the devtools package to install the development version:

## Make sure your current packages are up to date
update.packages()
## devtools is required
devtools::install_github("trinker/pacman")

Note: Windows users need Rtools and devtools to install this way.

More at https://github.com/trinker/pacman