Address of the bookmark: https://proksee.ca/

• nodes, which are labeled by sequences and ids
• edges, which connect two nodes via either of their respective ends
• paths, describe genomes, sequence alignments, and annotations (such as gene models and transcripts) as walks through nodes connected by edges

Address of the bookmark: https://github.com/vgteam/vg

Prerequisites

• A fresh Vultr Cloud Compute instance with Ubuntu 18.04 and root access.

Step 1: Install Apache, MySQL, and PHP

Elgg requires MySQL, PHP, and a web server. Before you can install Elgg, you will need to install the Apache web server, MySQL, and PHP.

Update the repository list.

apt-get update

Install the Apache web server.

apt-get install apache2 -y

Install MySQL.

apt-get install mysql-server -y

Complete the MySQL installation by executing the following command.

/usr/bin/mysql_secure_installation

During the installation, you will be asked to enter a root password. Enter a secure password. This will be the MySQL root password.

Would you like to setup VALIDATE PASSWORD plugin? [Y/N] N
New password: password
Re-enter new password: password
Remove anonymous users? [Y/N] Y
Disallow root login remotely? [Y/N] Y
Remove test database and access to it? [Y/N] Y
Reload privilege tables now? [Y/N] Y

Install PHP 7.2, as well as the PHP modules required by Elgg.

apt-get install php7.2 libapache2-mod-php7.2 php7.2-common php7.2-sqlite3 php7.2-curl php7.2-intl php7.2-mbstring php7.2-xmlrpc php7.2-mysql php7.2-gd php7.2-xml php7.2-cli php7.2-zip -y

Step 2: Create a MySQL database for Elgg

Elgg will require a MySQL database. Log into the MySQL console.

mysql -u root -p

When prompted for a password, enter the MySQL root password you set in step 1. Once you are logged in to the MySQL console, create a new database.

CREATE DATABASE elgg;

Create a new MySQL user and grant it privileges to the newly created database. You can replace username and password with the username and password of your choice.

GRANT ALL PRIVILEGES on elgg.* to 'username'@'localhost' identified by 'password';
FLUSH PRIVILEGES;

Exit the MySQL console.

exit

Step 3: Download and Install Elgg

Download the latest version of Elgg.

cd /var/www/html
rm -r index.html
wget https://elgg.org/download/elgg-2.3.7.zip

Unzip the downloaded archive and move the files to the root of the Apache web server.

apt install unzip
unzip elgg-2.3.7.zip
mv ./elgg-2.3.7/* . && rm elgg-2.3.7.zip && rm -r elgg-2.3.7

Create a data directory for Elgg.

sudo mkdir -p /var/www/html/data

Set the appropriate file permissions.

sudo chown -R www-data:www-data /var/www/html/
sudo chmod -R 755 /var/www/html/

Step 4: Configure Apache for Elgg

Elgg requires the Apache rewrite module. Enable the Apache rewrite module.

sudo a2enmod rewrite

Create an Apache configuration file for the Elgg installation.

sudo nano /etc/apache2/sites-available/elgg.conf

Paste the following snippet to the file, replacing example.com with your own domain name.

<VirtualHost *:80>
     DocumentRoot /var/www/html/
     ServerName example.com
     <Directory /var/www/html/>
          Options FollowSymlinks
          AllowOverride All
          Require all granted
     </Directory>
     ErrorLog ${APACHE_LOG_DIR}/error.log
     CustomLog ${APACHE_LOG_DIR}/access.log combined
</VirtualHost>

Enable the configuration and restart the Apache server.

 sudo a2ensite elgg.conf
 sudo systemctl restart apache2.service

• Assembly of nanopore reads using Canu.
• Polish canu contigs using racon (optional).
• Map a paired-end Illumina dataset onto the contigs obtained in the previous steps using BWA mem.
• Perform correction of contigs using pilon and the Illumina dataset.

Address of the bookmark: https://github.com/nanoporetech/ont-assembly-polish

• dnaPipeTE is developped by Clément Goubert, Laurent Modolo and the TREEP team of the LBBE: http://lbbe.univ-lyon1.fr/-Equipe-Elements-transposables-.html?lang=en

• You can find the original publication in GBE here: https://academic.oup.com/gbe/article/7/4/1192/533768

output examples of quantification and TE landscape (relative age) produced by dnaPipeTE

Address of the bookmark: https://github.com/clemgoub/dnaPipeTE

Ra is in development since 2014 in the form of several separate components that used to be run individually.
This project aims to ease the usage of Ra by integrating it into a complete de novo assembly tool.

Unlike other state-of-the-art assemblers, Ra does not have an error correction step. Instead, it relies on detecting overlaps using a very sensitive and specific overlapper ("graphmap -w owler", https://github.com/isovic/graphmap) and constructing and reducing an overlap graph (Ra layout, https://github.com/mariokostelac/ra).

Address of the bookmark: https://github.com/mariokostelac/ra-integrate/

Using AlignGraph

AlignGraph --read1 reads_1.fa --read2 reads_2.fa --contig contigs.fa --genome genome.fa --distanceLow distanceLow --distanceHigh distancehigh --extendedContig extendedContigs.fa --remainingContig remainingContigs.fa [--kMer k --insertVariation insertVariation --coverage coverage --part p --fastMap --ratioCheck --iterativeMap --misassemblyRemoval --resume]

Address of the bookmark: https://github.com/baoe/AlignGraph

The tool should be compatible with most UNIX flavors and has been successfully tested on the following operating systems:

• Mac OS X 10.11.1
• Mac OS X 10.10.3
• Ubuntu 14.04 LTS

Address of the bookmark: https://github.com/mculinovic/EAGLER