BOL: Related items

sunbeam: A robust, extensible metagenomics pipeline

Jit — Thu, 18 Jun 2020 06:58:52 -0500

Sunbeam is a pipeline written in snakemake that simplifies and automates many of the steps in metagenomic sequencing analysis. It uses conda to manage dependencies, so it doesn't have pre-existing dependencies or admin privileges, and can be deployed on most Linux workstations and clusters. To read more, check out our paper in Microbiome.

https://sunbeam.readthedocs.io/en/latest/

Address of the bookmark: https://github.com/sunbeam-labs/sunbeam

ContigExtender: a new approach to improving de novo sequence assembly for viral metagenomics data

LEGE — Wed, 08 May 2024 07:32:45 -0500

ContigExtender, was developed to extend contigs, complementing de novo assembly. ContigExtender employs a novel recursive Overlap Layout Candidates (r-OLC) strategy that explores multiple extending paths to achieve longer and highly accurate contigs. ContigExtender is effective for extending contigs significantly in in silico synthesized and real metagenomics datasets.

More at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7953547/

Address of the bookmark: https://github.com/dengzac/contig-extender

Workshop on population and metagenomics analysis @ NERC

Sun, 01 Dec 2013 14:25:45 -0600

Workshop Overview

A ten-day workshop taking place between 25 February - 6 March 2014 providing detailed hands-on training for population and meta-genomics analysis for researchers with little or no background in mathematics or computing.

Venue: Dartington Hall, Totnes, Devon (nearest train station - Totnes)

Times: 25 February - 6th March 2014.

Arrival evening of Tuesday 25 February 2014. Departure morning of 6th March 2014. The course itself will take place 9am-12pm, 2pm-5pm and on some evenings 7pm-10pm everyday 26 February-5th March. Students are expected to attend the entire course.

Contact: research-events@exeter.ac.uk

Registration

The course itself is free of charged and is funded by a Professional Postgraduate Development Award from NERC.

A total of 30 funded places are available which cover the costs of accommodation and food, but not the cost of transportation to/from the venue.

An additional 10 places are available for participants from industry. The cost of accommodation and meals will need to be covered by the participants.

You should register your interest by 31 December 2013. Participants will be informed by 10th January 2014 as to whether they have been selected. Please note that preference will be given to researchers funded by NERC.

More at http://www.eventbrite.co.uk/e/nerc-workshop-on-population-and-metagenomics-analysis-tickets-8628888237

iMAGine - in silico MetAGenomics pipeline

BioStar — Sat, 06 Jul 2024 04:32:18 -0500

iMAGine is a metagenomic workflow which includes filtering, assembling, and binning.

This workflow includes the following tools which are needed to be installed in the system.

Address of the bookmark: https://github.com/avishekdutta14/iMAGine

World of Omics

Rahul Agarwal — Tue, 16 Jul 2013 17:11:48 -0500

How many variants of "omics" techniques presently in use ?

Should you get sequenced? Not all bad genes predict disease

Rahul Agarwal — Thu, 29 Aug 2013 15:10:53 -0500

“What we really don’t know yet is whether the predictive aspects of the genome are going to turn out to be beneficial or potentially harmful”

“As we roll out genomic medicine we are fighting against this society-wide misconception that having the bad gene means you’re going to get the disease. That’s only true in a very few cases.”

Source:Today Health

Address of the bookmark: http://www.today.com/health/should-you-get-sequenced-not-all-bad-genes-predict-disease-8C11017154

320000 viruses in mammals yet to sequenced in future!!!

Rahul Agarwal — Tue, 03 Sep 2013 08:35:30 -0500

With current biological technique improvements, finally it is now possible to look at millions of unknown viruses at genomic level and understand the mechanism. According to available data, close to 70 per cent of emerging viral diseases such as HIV/AIDS, West Nile, Ebola, SARS, and influenza, are zoonoses - infections of animals that cross into humans.

To address the challenges of describing and estimating virodiversity, a team of investigators from Center for Infection and Immunity (CII) and EcoHealth Alliance began in jungles of Bangladesh - home to the flying fox.

Reference:

http://economictimes.indiatimes.com/news/news-by-industry/et-cetera/mammals-harbour-at-least-320000-new-viruses/articleshow/22253268.cms

http://www.bbc.co.uk/news/science-environment-23932400

RNA Bioinformatics and High Throughput Analysis Jena

Sat, 09 Nov 2013 20:03:56 -0600

Research Topics:

High Throughput Sequencing Analysis
Comparative Genomics
Identification and Annotation of Non-coding RNAs
Bioinformatic Analysis and System Biology of Viruses
Coevolution of Proteins and RNAs
Algorithmic Bioinformatics
Phylogenetic Analysis

http://www.rna.uni-jena.de/index.php

Bio-Rad Acquires GnuBIO

Rahul Agarwal — Sat, 19 Apr 2014 10:36:36 -0500

http://www.businesswire.com/news/home/20140411005331/en/Bio-Rad-Acquires-GnuBIO-Developer-Droplet-Based-DNA-Sequencing#.U1KXnPm1b8o

Deadly Human Pathogen Cryptococcus Sequenced

Rahul Agarwal — Fri, 25 Apr 2014 11:02:21 -0500

"Now, researchers have sequenced the entire genome and all the RNA products of the most important pathogenic lineage of Cryptococcus neoformans, a strain called H99. The results, which appear in PLOS Genetics, also describe a number of genetic changes that can occur after laboratory handling of H99 that make it more susceptible to stress, hamper its ability to sexually reproduce and render it less virulent."

Source:

http://www.biosciencetechnology.com/news/2014/04/deadly-human-pathogen-cryptococcus-fully-sequenced

Paper:

http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1004292