BOL: Related items

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

SimLoRD: A read simulator for third generation sequencing reads

Aaryan Lokwani — Wed, 22 Aug 2018 10:40:27 -0500

SimLoRD is a read simulator for third generation sequencing reads and is currently focused on the Pacific Biosciences SMRT error model.

Reads are simulated from both strands of a provided or randomly generated reference sequence.

The reference can be read from a FASTA file or randomly generated with a given GC content. It can consist of several chromosomes, whose structure is respected when drawing reads. (Simulation of genome rearrangements may be incorporated at a later stage.)
The read lengths can be determined in four ways: drawing from a log-normal distribution (typical for genomic DNA), sampling from an existing FASTQ file (typical for RNA), sampling from a a text file with integers (RNA), or using a fixed length
Quality values and number of passes depend on fragment length.
Provided subread error probabilities are modified according to number of passes
Outputs reads in FASTQ format and alignments in SAM format

Address of the bookmark: https://bitbucket.org/genomeinformatics/simlord/

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/

wtdbg2: A fuzzy Bruijn graph approach to long noisy reads assembly

BioStar — Mon, 04 Feb 2019 04:53:47 -0600

Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output.

./wtdbg2 -x rs -g 4.6m -t 16 -i reads.fa.gz -fo prefix
./wtpoa-cns -t 16 -i prefix.ctg.lay.gz -fo prefix.ctg.fa

Address of the bookmark: https://github.com/ruanjue/wtdbg2

Free Genomics data !

BioStar — Fri, 07 Feb 2020 14:08:31 -0600

The specimens were collected by the Oxford Wytham Woods and Edinburgh Lohse lab teams. DNA extraction and sequencing was carried out by the Sanger Institute Scientific Operations teams. Assemblies were carried out by the Tree of Life team (Shane McCarthy) and colleagues in Pacific Biosciences (Jonas Korlach).

https://www.darwintreeoflife.org/an-initial-set-of-raw-genome-assemblies-from-the-darwin-tree-of-life-project/

Address of the bookmark: https://www.darwintreeoflife.org/an-initial-set-of-raw-genome-assemblies-from-the-darwin-tree-of-life-project/

SRF/JRF Bioinformatics at National Bureau of Animal Genetic Resources

Thu, 26 Nov 2015 01:54:07 -0600

National Bureau of Animal Genetic Resources

SRF Job vacancies in National Bureau of Animal Genetic Resources (NBAGR) on contractual basis

No. of Posts : 03

Qualifications : Master degree in any one of discipline/ Subjects Biotechnology/Bioinformatics/Life Sciences/ Computer Applications with 4 years/5 years of Bachelor’s degree. Candidates having post graduate degree in above mentioned subjects with 3 years Bachelor’s degree should be NET qualified.

Note : i. The Ph.D. Degree holders are eligible for the posts. ii. The Master’s degree holders with the integrated degrees like B.Tech. & M. Tech. (5 years) are eligible. iii. Graduates with three years Bachelor’s degree, who have acquired professional Master’s degree (3 years) like M.Sc. (Ag.), Masters in Computer Applications, M. Tech., etc., are eligible.

Desirable : The candidates should have zeal to work in R environment and NGS data analysis

Emolument : Rs. 28,000/-

Age Limit : 35 year for Men and 40 years for Women in case of SRF on the date of Interview.
How to apply

Walk-in-Interview is proposed to be held at National Bureau of Animal Genetic Resources, Karnal (Haryana)-132 001 at 10:30 AM on 02.12.2015. Interested candidates may attend Walk-in-Interview at 10:30 AM on 02.12.2015 alongwith original certificates and typed bio-data with one set of attested copies of each their certificates with passport size photograph.

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

CIAB Recruits Scientist, Engineer, Informatics Officer

Sat, 28 Nov 2015 03:40:28 -0600

Center of Innovative and Applied Bioprocessing (CIAB) - Punjab

Center of Innovative and Applied Bioprocessing (CIAB) invites applications to recruit on vacant posts of Scientist, Associate Plant Manager/ Plant Engineer, Informatics Officer. Applications against these Government Jobs can be submitted on or before 7th January 2016.
CIAB Vacancy 2015 Details

9. Research & Development – Informatics Officer
Qualification: M. Tech or M.E. in computer science or information technology or bioinformatics with 4 years of R&D experience (after Master’s Degree) in an R&D organization with work profile of large data assembly, analysis.
Age Limit: 45 years
How to Apply : Duly filled-in applications in prescribed application format along with copies of required documents should be reach to: Chief Exec

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

Jit — Thu, 24 Dec 2020 10:03:36 -0600

Hifiasm is a fast haplotype-resolved de novo assembler for PacBio Hifi reads. It can assemble a human genome in several hours and works with the California redwood genome, one of the most complex genomes sequenced so far. Hifiasm can produce primary/alternate assemblies of quality competitive with the best assemblers. It also introduces a new graph binning algorithm and achieves the best haplotype-resolved assembly given trio data.

Address of the bookmark: https://github.com/chhylp123/hifiasm

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