BOL: Related items

Do you think it's important for everyone to pass BINC exam?

Jit — Wed, 11 May 2016 07:25:34 -0500

The Department of Biotechnology (DBT), Government of India has instituted BINC examination with the objective of evaluating the Bioinformatics knowledge & skills of students. Do you think it is important ?

Sample BINC question paper 2016 - part1

Radha Agarkar — Fri, 13 May 2016 03:41:48 -0500

Please download the sample bioinformatics question paper for BINC 2016

Platanus

Jit — Fri, 13 May 2016 05:12:40 -0500

Platanus is a novel de novo sequence assembler that can reconstruct genomic sequences of
highly heterozygous diploids from massively parallel shotgun sequencing data.

The latest version is 1.2.4.

To cite Platanus, please use the following:

Kajitani R, Toshimoto K, Noguchi H, Toyoda A, Ogura Y, Okuno M, Yabana M, Harada M, Nagayasu E, Maruyama H, Kohara Y, Fujiyama A, Hayashi T, Itoh T, “Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads”. Genome Res. 2014 Aug;24(8):1384-95. doi: 10.1101/gr.170720.113. [abstract | full text]

Address of the bookmark: http://platanus.bio.titech.ac.jp/

MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping

Neel — Fri, 20 May 2016 18:53:49 -0500

MOSAIK is a stable, sensitive and open-source program for mapping second and third-generation sequencing reads to a reference genome. Uniquely among current mapping tools, MOSAIK can align reads generated by all the major sequencing technologies, including Illumina, Applied Biosystems SOLiD, Roche 454, Ion Torrent and Pacific BioSciences SMRT. Indeed, MOSAIK was the only aligner to provide consistent mappings for all the generated data (sequencing technologies, low-coverage and exome) in the 1000 Genomes Project. To provide highly accurate alignments, MOSAIK employs a hash clustering strategy coupled with the Smith-Waterman algorithm. This method is well-suited to capture mismatches as well as short insertions and deletions. To support the growing interest in larger structural variant (SV) discovery, MOSAIK provides explicit support for handling known-sequence SVs, e.g. mobile element insertions (MEIs) as well as generating outputs tailored to aid in SV discovery.

Address of the bookmark: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0090581

Senior Project Fellow Bioinformatics at NBRI

Sat, 21 May 2016 21:01:05 -0500

Walk In Interview No. 03/Project/2016
Senior Project Fellow Bioinformatics Job vacancies in CSIR- National Botanical Research Institute (NBRI), Lucknow
Area III: Molecular Biology & Biotechnology
Qualification : 1st Class M.Sc. in Bioinformatics/Biotechnology/ Life Science /Biochemistry/Botany with 2 years research experience and at least one publication in SCI Journal or 1st class M.Tech in Bioinformatics
Age : 32 years
Salary : Rs.18000
How to apply
Date & Venue of Interview For Area III: 27-05-2016 at 11.00 A.M. at Conference Room, T.N. Khushoo Block, NBRI, Lucknow.

http://www.nbri.res.in/temp.php

Research Associate Bioinformatics at MANIT

Thu, 26 May 2016 02:20:58 -0500

Research Associate Jobs opportunity in Maulana Azad National Institute of Technology (MANIT) on contract basis
Project : “Screening of Anti-venom potential of medicinal plants from Tribal region of Madhya Pradesh"
No. of Post : 01

Qualification : The minimum qualifications are : Ph.D in Bioinformatics/ Biotechnology or allied branches with atleast two publication in SCI journals.
Fellowship : The consolidated emoluments of Rs.36, 000/ PM+HRA+MA as per CSIR rules.

How to apply
Applications (in prescribed attached format and supporting documents) to be received in the Dr. Rahul Shrivastava, Principal Investigator (CSIR Project), Department of Biological Science and Engineering, Maulana Azad National Institute of Technology, Bhopal – 462003 (MP) on or before 7th June 2016.

More at http://www.web.manit.ac.in/Year%202016/Recruitment%20Contract%20Faculty/Biological/Advertisement%20for%20Antivenome%20project%202.pdf

Assistant Professor Bioinformatics / Teaching Assistant at Gujarat University

Sat, 04 Jun 2016 16:04:26 -0500

Assistant Professor Bioinformatics / Teaching Assistant Jobs recruitment in Gujarat University
Departments :

M.Sc. Bioinformatics Climate Change and Impacts Management
M.Sc. Biotechnology and Clinical Research

Department of Computer Science (Rollwala Computer Centre)
Appointment will be on purely contract basis for 11 months on consolidated salary. Reservation as per rules

How to apply
All the candidate are here by required to fill up the application form and given to concern Department, Gujarat University, Ahmedabad (Form can be submitted personally or thorough post/courier.) Candidates are supposed to attach the self attested photocopies of their required testimonials along with application form. Last date of receipt of application is 10/06/2016.

More http://www.gujaratuniversity.org.in/web/NWD/NewsEvents/1700_Recruitments%20at%20Gujarat%20University.asp

Blobology

Jit — Mon, 13 Jun 2016 10:18:33 -0500

Tools for making blobplots or Taxon-Annotated-GC-Coverage plots (TAGC plots) to visualise the contents of genome assembly data sets as a QC step

Blaxter Lab, Institute of Evolutionary Biology, University of Edinburgh

Goal: To create blobplots or Taxon-Annotated-GC-Coverage plots (TAGC plots) to visualise the contents of genome assembly data sets as a QC step.

This repository accompanies the paper:
Blobology: exploring raw genome data for contaminants, symbionts and parasites using taxon-annotated GC-coverage plots. Sujai Kumar, Martin Jones, Georgios Koutsovoulos, Michael Clarke, Mark Blaxter
(submitted 2013-10-01 to Frontiers in Bioinformatics and Computational Biology special issue : Quality assessment and control of high-throughput sequencing data).

It contains bash/perl/R scripts for running the analysis presented in the paper to create a preliminary assembly, and to create and collate GC content, read coverage and taxon annotation for the preliminary assembly, which can be visualised, such as Figure 2a from the paper showing TAGC plots/blobplots for Caenorhabditis sp. 5:

Address of the bookmark: https://github.com/blaxterlab/blobology

KisSplice

Jit — Tue, 16 Aug 2016 08:34:19 -0500

KisSplice is a software that enables to analyse RNA-seq data with or without a reference genome. It is an exact local transcriptome assembler that allows to identify SNPs, indels and alternative splicing events. It can deal with an arbitrary number of biological conditions, and will quantify each variant in each condition. It has been tested on Illumina datasets of up to 1G reads. Its memory consumption is around 5Gb for 100M reads.

KisSplice is not a full-length transcriptome assembler. This means that it will output the variable regions of the transcripts, not reconstruct them entirely.

KisSplice comes as a workflow, with several possible post-treatments meant to facilitate the analysis of the results. The choice of the post-treatment depends on the availability of a reference genome/transcriptome and on the need to perform a differential analysis, as summarised in the following table.

Address of the bookmark: http://kissplice.prabi.fr/

A5-miseq

Jit — Thu, 18 Aug 2016 04:05:23 -0500

_A5-miseq_ is a pipeline for assembling DNA sequence data generated on the Illumina sequencing platform. This README will take you through the steps necessary for running _A5-miseq_.

Point to note:

There are many situations where A5-miseq is not the right tool for the job. In order to produce accurate results, A5-miseq requires Illumina data with certain characteristics. A5-miseq will likely not work well with Illumina reads shorter than around 80nt, or reads where the base qualities are low in all or most reads before 60nt. A5-miseq assumes it is assembling homozygous haploid genomes. Use a different assembler for metagenomes and heterozygous diploid or polyploid organisms. Use a different assembler if a tool like FastQC reports your data quality is dubious. You have been warned! Datasets consisting solely of unpaired reads are not currently supported.

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