BOL: Related items

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

Seal: SEquence ALignment evaluation suite

Jit — Wed, 03 Jan 2018 05:05:46 -0600

Seal is a comprehensive sequencing simulation and alignment tool evaluation suite. This software (implemented in Java) provides several utilities that can be used to evaluate alignment algorithms, including:

Reading a pre-existing reference genome from one or more FASTA files.
Alternatively, generating an artificial reference genome based on input parameters (length, repeat count, repeat length, repeat variability rate).
Simulating reads from random locations in the genome based on input parameters of read length, coverage, sequencing error rate, and indel rate.
Applying alignment tools to the genome and the reads through a standardized interface.
Parsing the output of the alignment tool and calculating the number of reads that were correctly or incorrectly mapped.
Computing run times and measures of accuracy.

Seal has interfaces to evaluate the following software packages:

Bowtie
BWA
MAQ
mrFAST
mrsFAST
Novoalign
SHRiMP
SOAPv2

Address of the bookmark: http://compbio.case.edu/seal/

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.

gfastats: The swiss army knife for genome assembly.

Abhi — Thu, 08 Sep 2022 06:03:05 -0500

gfastats is a single fast and exhaustive tool for summary statistics and simultaneous *fa* (fasta, fastq, gfa [.gz]) genome assembly file manipulation. gfastats also allows seamless fasta<>fastq<>gfa[.gz] conversion. It has been tested in genomes even >100Gbp.

Address of the bookmark: https://github.com/vgl-hub/gfastats

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

BBSplit: Read Binning Tool for Metagenomes and Contaminated Libraries

Poonam Mahapatra — Wed, 03 Jan 2018 00:25:27 -0600

BBSplit internally uses BBMap to map reads to multiple genomes at once, and determine which genome they match best. This is different than with ordinary mapping. If a genome (say, human) contains an exact repeat somewhere, reads mapping to it will be mapped ambiguously. But if you want to determine whether reads are mouse or human, it does not matter whether they map ambiguously within human, only whether they are ambiguous between human and mouse. BBSplit tracks this additional ambiguity information and decides how to use it based on the “ambig2” flag. The normal use of BBSplit is like Seal, either quantifying how many reads go to each reference, or splitting the reads into multiple output files, one per reference. BBSplit can only be run using references indexed with BBSplit, as they contain additional information regarding which sequences came from which reference file.

BBSplit is a tool that bins reads by mapping to multiple references simultaneously, using BBMap. The reads go to the bin of the reference they map to best. There are also disambiguation options, such that reads that map to multiple references can be binned with all of them, none of them, one of them, or put in a special "ambiguous" file for each of them. Paired reads will always be kept together.

For example, if you had a library of something that was contaminated with e.coli and salmonella, you could do this:

bbsplit.sh in=reads.fq ref=ecoli.fa,salmonella.fa basename=out_%.fq outu=clean.fq int=t

This will produce 3 output files:
out_ecoli.fq (ecoli reads)
out_salmonella.fq (salmonella reads)
clean.fq (unmapped reads)

In this case, "int=t" means that the input file is paired and interleaved. For single-end reads you would leave that out. For paired reads in 2 files, you would do this:
bbsplit.sh in1=reads1.fq in2=reads2.fq ref=ecoli.fa,salmonella.fa basename=out_%.fq outu1=clean1.fq outu2=clean2.fq

BBSplit is available here:
https://sourceforge.net/projects/bbmap/

The sensitivity can be raised to be equivalent to BBMap with these flags: "minratio=0.56 minhits=1 maxindel=16000"

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.

CViT: Chromosome Viewing Tool

Rahul Nayak — Wed, 02 Jan 2019 04:10:09 -0600

CViT - Chromosome Viewing Tool. A collection of Perl scripts that enable quick visualizations of features on linkage groups, psuedochromosomes or cytogenetic maps. Intended for whole-genome views of data but can be used to create images of single chromosomes/linkage groups, contigs, or BACs, or even proteins -- any feature that has a location on a backbone. Handles most standard genetic/genomic coordinate systems. Reads GFF3 data and produces a PNG or SVG image.

https://www.hindawi.com/journals/ijpg/2011/373875/

Address of the bookmark: https://sourceforge.net/projects/cvit/

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

QuasR: Quantification and annotation of short reads in R

Neel — Fri, 13 Aug 2021 07:44:05 -0500

The QuasR package (short for Quantify and annotate short reads in R) integrates the functionality of several R packages (such as IRanges (Lawrence et al. 2013) and Rsamtools) and external software (e.g. bowtie, through the Rbowtie package, and HISAT2, through the Rhisat2 package). The package aims to cover the whole analysis workflow of typical high throughput sequencing experiments, starting from the raw sequence reads, over pre-processing and alignment, up to quantification. A single R script can contain all steps of a complete analysis, making it simple to document, reproduce or share the workflow containing all relevant details.

Address of the bookmark: https://www.bioconductor.org/packages/devel/bioc/vignettes/QuasR/inst/doc/QuasR.html