MeGAMerge (A tool to merge assembled contigs, long reads from metagenomic sequencing runs)

Description

MeGAMerge is a perl based wrapper/tool that can accept any number of sequence (FASTA) files containing assembled contigs of any length in Multi-FASTA format to produce an improved contig set based on OLC based assembly. All overlap parameters (Minimum Overlap Length, Identity, etc) are user-declarable at runtime. It is written to run on Linux.

Requirements:

You will need to have the following tools installed and in $PATH, or added to $binpath in the tool:

Newbler (specifically runAssembly)
Minimus2 (part of AMOS, also requires MUMmer)

Address of the bookmark: https://github.com/LANL-Bioinformatics/MeGAMerge

More at
https://zfin.org/ZDB-LAB-110408-1
http://www.imcb.a-star.edu.sg/php/venkatesh.php

SYMPOSIUM DESCRIPTION: Genomics of Adaptation [S16] Model organisms for life-history research are mainly studied in the lab where functional genetics is assessable. In general, however, knowledge about their eco-evolutionary dynamics, such as biotic interactions, is rare. By contrast, in organisms for which the ecology and adaptation strategies in the field are well known, we typically lack the appropriate genetic tools to investigate functionality. Advances in genomics and statistics as well as investments in evolutionary model organisms are now providing access to putatively adaptive genome-wide variation within species from across the tree of life. In this symposium, we focus on integrating life-history biology, genetics and evolutionary ecology in the genomics era.

We wish to (1) highlight the role of genetic architecture of complex traits, such as adaptations to biotic interactions or life-history traits; (2) contrast this to morphological traits which are generally thought to have a less complex genetic architecture; and (3) discuss the opportunities and drawbacks of specific model systems.

INVITED SPEAKERS: Josephine Pemberton, University of Cambridge (http://bit.ly/2hJWytJ ) Peter Tiffin, University of Minnesota (http://bit.ly/2hK7HuS )

ABSTRACT SUBMISSION The deadline for abstract submission is January 10, 2017. For more information and to submit abstracts online, please visit: http://bit.ly/2fBXlvN We look forward to an exciting symposium and seeing you all in Groningen! Sincerely, Ben Blackman, UC Berkeley Maaike de Jong, University of Bristol Bart Pannebakker, Wageningen University Noah Whiteman, UC Berkeley Jelle Zandveld, Wageningen University

You will need to solve bioinformatics problems using programming. The goal is to correctly solve as many problems as possible within 24 hours. Some of them will be approximation problems and will have partial grades. All rounds will be held online, submissions will be auto-graded in real time.

Check more at http://contest.bioinf.me/

Good luck!

Progressive Cactus is a whole-genome alignment package.

Requirements

• git
• gcc 4.2 or newer
• python 2.7
• wget
• 64bit processor and build environment
• 150GB+ of memory on at least one machine when aligning mammal-sized genomes; less memory is needed for smaller genomes.
• Parasol or SGE for cluster support.
• 750M disk space

Instructions

IMPORTANT NOTE: Progressive Cactus does not presently support installation into paths that contain spaces. Until this is resolved, you can use a softlink as a workaround: ln -s "path with spaces" "installation path without spaces"

In the parent directory of where you want Progressive Cactus installed:

git clone git://github.com/glennhickey/progressiveCactus.git
cd progressiveCactus
git pull
git submodule update --init
make

It is also convenient to add the location of progressiveCactus/bin to your PATH environment variable. In order to run the included tools (ex hal2maf) in the submodules/ directory structure, first source progressiveCactus/environment to load the installed environment.

If any errors occur during the build process, you are unlikely to be able to use the tool. Please submit a GitHub issue so we can help out: not only will you help yourself, but others who wish to use the tool as well.

Note that all dependencies are also built and included in the submodules/ directory. This increases the size and build time but greatly simplifies installation and version management. The installation does not create or modify any files outside the progressiveCactus/ directory.

Address of the bookmark: https://github.com/glennhickey/progressiveCactus

Applicant are required to bring applications on plain paper, stating the name, address, date of birth. educational qualifications and experiences and Institute, along with attested photocopies of mark sheets and certificates etc. at the time of Interview. Applications should also be sent by Entail to Dr. Madhu Chopra, Coordinator, BIF Facility. Email: acbrdu.blisnet@nic.in; mchopradu@gmail.com.
Interview Date : 13.02.2017
Time : 10:00 am-12:00 noon
Venue : ACBR

Distribution package for the Prgressive Cactus multiple genome aligner. Dependencies are linked as submodules

https://github.com/glennhickey/progressiveCactus

Address of the bookmark: https://github.com/glennhickey/progressiveCactus

There are several pre-computed trees available for display, including the main Tree Of Life, described in Ciccarelli, et al., 2006. In addition to the precomputed trees, users can upload and display personal trees and data, using the 'Data upload' page or through a personal user account.

Address of the bookmark: http://itol.embl.de/

The corresponding publication can be found here:

B. Voss*, M. Hanselmann*, B.Y. Renard, M.S. Lindner, U. Köthe, M. Kirchner, F.A. Hamprecht (2011). SIMA: Simultaneous Muliple Alignment of LC/MS Peak Lists, Bioinformatics 27(7):987-993. [doi] [techreport]

Address of the bookmark: https://hciweb.iwr.uni-heidelberg.de/hci/softwares/sima

Lab https://www.ieo.it/en/RESEARCH/People/Researchers/Pasini-Diego/