The Role

We are looking for a Software Engineer - Computational Biologist with 3+
years' experience in a similar role to design and implement a backend system
to support an online individualised genomics interface. This position is a
great opportunity for an ambitious, self-motivated individual to work in a
demanding, challenging and interesting role.

Position Description:
. Participate in planning, design, and implementation of Equinome back
end systems and technologies.
. Implement interfaces and management tools for back end services.
. Manage, analyse, interpret and visualise large genomics data sets.
. Work closely with scientific team to develop new features and
application enhancements
. Design, develop and manage a genomics research database.

Qualification/Experience:
. Minimum MSc in Computer Science, Genetics, Bioinformatics or in a
related field (A Ph.D qualification would be an advantage).
. Proven 3+ years of experience in similar role.
. Highly proficient in Python, SQL, MySQL.
. Excellent knowledge of mammalian genomics, bioinformatics and
statistical/population genetics.
. Hands-on experience working with large data sets.
. Experience with front-end technologies (HTML/CSS/Javascript) an
advantage.
. Experience in rapid web application development: e.g. Django.
. Knowledge or experience of Unix Scripting and R statistical
programming language would be an advantage.
. Ability to work with minimum supervision to deliver high-quality
code on time.
. Fluency in English and good written and communication skills.
. Meticulous attention to detail.

Applications should be submitted before Friday, 26 September 2014 using the
following link:
http://bit.ly/WgbhxS

Note: Full information and application procedure is available at this link:
http://bit.ly/WgbhxS

ABySS Explorer

Interactive Java application that uses a novel graph-based representation to display a sequence assembly and associated metadata

http://www.bcgsc.ca/platform/bioinfo/software/abyss-explorer

BamView

Genome browser and annotation tool that allows visualization of sequence features, next-generation sequencing (NGS) data and the results of analyses within the context of the sequence, and also its six-frame translation

http://www.sanger.ac.uk/resources/software/artemis/

DNannotator 

Annotation web toolkit for regional genomic sequences

http://bioapp.psych.uic.edu/DNannotator.htm

JVM 

Java Visual Mapping tool for NGS reads

http://www.springer.com/cda/content/document/cda_downloaddocument/9789401792448-c2.pdf?SGWID=0-0-45-1487072-p176815501

LookSeq 

Web-based visualization of sequences derived from multiple sequencing technologies. Low- or high-depth read pileups and easy visualization of putative single nucleotide and structural variation

http://lookseq.sourceforge.net

MagicViewer 

Visualization of short read alignment, identification of genetic variation and association with annotation information of a reference genome

http://bioinformatics.zj.cn/magicviewer/

MapView 

Alignments of huge-scale single-end and pair-end short reads

http://omictools.com/mapview-s1367.html

MultiPipMaker

Computes alignments of similar regions in two DNA sequences. The resulting alignments are summarized with a ‘percent identity plot’ (pip)

http://pipmaker.bx.psu.edu/pipmaker/

PileLineGUI 

Handling genome position files in NGS studies

http://sing.ei.uvigo.es/pileline/pilelinegui.html

SAMtools tview 

Simple and fast text alignment viewer; NGS compatible

http://www.htslib.org/

SEWAL

Uses a locality-sensitive hashing algorithm to enumerate all unique sequences in an entire Illumina sequencing run

http://www.sourceforge.net/projects/sewal

STAR 

A web-based integrated solution to management and visualization of sequencing data

http://wanglab.ucsd.edu/star/browser

SVA 

Software for annotating and visualizing sequenced human genomes

http://www.svaproject.org

Viewer (IGV) 

Visualization of large heterogeneous datasets, providing a smooth and intuitive user experience at all levels of genome resolution

https://www.broadinstitute.org/igv/

ZOOM Lite 

NGS data mapping and visualization software

http://bioinfor.com/zoom/lite/

Eligibility:
M.Sc. in any stream of Life Sciences with minimum 55% marks.

Desirable:
Candidates having experience in Molecular Spectroscopy, Protein Folding and Bioinformatics will be preferred.

Interested candidate may appear in the walk in Interview conducted on September 16, 2014 (Tuesday) 11:00 AM in the Director's Office, Centre for Interdisciplinary Research in Basic Sciences, lamia Millia Islamia, New Delhi-110025.
Candidates are required to bring a set of Xerox copy of their recent CV and qualifying degree (certificate/mark sheet) along with original documents. NoTA/DA will be paid.

For any further information you may e-mail to: mihassan@jmLac.in

Read more at http://jmi.ac.in/upload/advertisement/jobs_cirbs_2014september8.pdf

Take a look at the PRICE software from the DeRisi lab. Its meant to do something very similar. http://derisilab.ucsf.edu/index.php?page=software

You could also look at SSPACE (http://www.baseclear.com/landingpages/basetools-a-wide-range-of-bioinformatics-solutions/sspacev12/), ATLAS tools (http://www.hgsc.bcm.tmc.edu/content/bcm-hgsc-software), and SCARPA (http://compbio.cs.toronto.edu/hapsembler/scarpa.html).

See the PAGIT protocol: http://www.sanger.ac.uk/resources/software/pagit/

In particular, take a look at the IMAGE tool: http://genomebiology.com/2010/11/4/R41

Also SOAPdenovo has ha function for scaffolding. Not sure about ABYSS

Here there is a useful explanation of several tools.

https://bioinformaticsonline.com/search?q=scaffolding&entity_type=object&entity_subtype=bookmarks&offset=0&search_type=entities

I could be wrong, but the above answers to your hypothetical scenario appear to miss the point that you aren't interested in assembling the full genome, just the 100 kb part you're interested in. I suggest the following algorithm:

1. Start with the initial assembly C0 of the contigs you have identified as overlapping your region of interest, and the set S of reads those contigs contain. Let C = C0.

2. Repeat:
a. Identify paired-end reads (not in C) for which one or both ends align within, or extending, contigs in C.
b. Identify unpaired reads that align extending these new paired-end reads.
c. Construct a new assembly C' from C and the new reads identified in (a) and (b).
d. Trim C' so it does not extend more than 100 kb to either end of C0. Set C = C'.
e. Let S' denote the reads that contribute to C'. If S' does not contain any reads not present in S, stop. Otherwise, Set S = S'.

3. If you don't have a complete assembly of the region of interest, generate an STS for each end of each contig, probe a library for clones including these STSes, subclone these clones into a paired-end sequencing vector, and generate paired-end reads for this library; then try steps (1) and (2) again, adding these new sequencing reads to what you had before.

4. If your average sequencing depth for the region of interest exceeds 25 or so without filling all gaps, it is likely that the remaining gaps represent sequences that are not getting cloned in your sequencing vectors. Try different sequencing vectors.

(Deemed University)

Hamdard Nagar, New Delhi – 110 062

R E C R U I T M E N T

(Advertisement No. 5/2014)

Applications on prescribed form are invited for filling up the following teaching positions in the Department of Biotechnology, Faculty of Science in the university. Eligible candidates may apply on or before 30.09.2014.

1. Professor/Associate Professor - One in Pay Band of Rs. 37400-67000+ AGP Rs.10000/9000

2. Assistant Professor - Two in Pay Band of Rs. 15600-39100+ AGP Rs. 6000/-

ASSISTANT PROFESSOR – 02 (including 01 SFS)

Specialization : Bioinformatics

Qualification and Experience :

Ph.D. in Biotechnology or an allied discipline with M.Sc. in Biotechnology/ Biochemistry in the First division or equivalent grade from a recognized University/ Institute.

NET in Life Science or allied discipline in addition to the above qualification.

Experience : At least two years of Post-doctoral teaching and/or research experience in Bioinformatics or relevant field in a UGC recognized Institution of repute or international research institute/ University. Proof of research to be evidenced by publications in SCI-indexed journals of high impact factor as the first or corresponding author.

Note : University may consider exempting candidates from NET, who has been awarded Ph.D. degree from ‘A’ Grade accredited University following the procedure as notified by the UGC in its Regulations of 2009 and adopted by Jamia Hamdard.

For more information: http://www.jamiahamdard.ac.in/PDF/Online%20application%20form%20_Teaching_1.pdf
http://www.jamiahamdard.ac.in/PDF/PBAS.pdf

Address of the bookmark: https://www.molinspiration.com/

Functional and Comparative Genomics

http://jp.senescence.info/
http://www.senescence.info/
http://www.liv.ac.uk/integrative-biology/staff/joao-de-magalhaes/

More at https://dahak-metagenomics.github.io/dahak/

Address of the bookmark: https://github.com/dahak-metagenomics/dahak

Extent of employment: 30 Hours per Week
Duration of employment: 1st of October 2015 to 30th of September 2019
Gross monthly salary and pay grade in terms of collective agreement for university staff (payable 14 times per year): B1, € 1.997,20

Responsibilities
The successful candidate (f/m) will pursue a Ph.D. project related to the interpretation of plant genome and transcriptome sequencing data from next-generation sequencing (NGS) platforms. In particular, the candidate will characterize the unexplored genome of quinoa, a crop plant of long-standing tradition in Latin America. We collaborate with research partners in Austria and abroad, and the candidate’s project will be of central importance in the context of this research network.

Required skills and qualifications
We are looking for a graduate student (f/m) with a Master’s degree in bioinformatics or in a related field, solid programming skills (e.g. developing sequence analysis tools), experience with the analysis of NGS data sets, understanding of lab methods and knowledge of genomics/transcriptomics. The group has successfully performed several projects using NGS technology. We have recently published the reference genome sequence of sugar beet (Dohm et al., Nature, 2014), a crop plant closely related to quinoa (same family, but different genus). Not yet published is a quinoa genome assembly that we have generated, and which will serve as the starting point of the candidate’s project. We are a multidisciplinary team and offer work in a lively and friendly atmosphere, and state-of-the-art computing infrastructure. We are looking forward to expanding our team by a dedicated and strongly motivated person with a distinct interest in the challenges of plant genomics.

Applications can be submitted until: 16th of August 2015

University of Natural Resources and Life Sciences Vienna seeks to increase the number of its female faculty and staff members. Therefore qualified women are strongly encouraged to apply. In case of equal qualification, female candidates will be given preference unless reasons specific to an individual male candidate tilt the balance in his favour.

Please send your job application (incl. letter of motivation, CV, summary of Master’s thesis and contact details for two referees) to Personnel department, University of Natural Resources and Life Sciences, 1190 Vienna, Peter-Jordan-Straße 70; E-Mail: kerstin.buchmueller@boku.ac.at. (Reference code: 59)

We regret that we cannot reimburse applicants travel and lodging expenses incurred as part of the selection and hiring process.

www.boku.ac.at

Reference:

https://www.pacb.com/blog/young-investigators-share-stellar-science-career-advice-and-bioinformatics-tools-at-smrt-leiden-2021/