http://www.gigasciencejournal.com/content/2/1/10/abstract

http://blogs.nature.com/news/2013/07/genome-assembly-contest-prompts-soul-searching.html

http://assemblathon.org/post/44431915644/feedback-and-analysis-of-the-assemblathon-2-p

2. Parallel sequencing lives, or what makes large sequencing projects successful https://academic.oup.com/gigascience/article/6/11/gix100/4557140?login=false

3. Common-sense approaches to sharing tabular data alongside publication https://www.sciencedirect.com/science/article/pii/S2666389921002300

4. A Reproducible Data Analysis Workflow with R Markdown, Git, Make, and Docker https://psyarxiv.com/8xzqy/

5. Practical Computational Reproducibility in the Life Sciences https://www.cell.com/cell-systems/fulltext/S2405-4712(18)30140-6

6. A video by Dr.Keith A. Baggerly from MD Anderson [The Importance of Reproducible Research in High-Throughput Biology](https://www.youtube.com/watch?v=7gYIs7uYbMo) highly recommended.

7. Ten Simple Rules for Reproducible Computational Research http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003285)

8. Good Enough Practices in Scientific Computing http://arxiv.org/abs/1609.00037 

9. Best Practices for Scientific Computing https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001745

10. A Quick Guide to Organizing Computational Biology Projects http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.100042  A must read for computational biologists!

11. Reproducibility of computational workflows is automated using continuous analysis https://www.nature.com/articles/nbt.3780

12. Five selfish reasons to work reproducibly https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0850-7

https://www.forbio.uio.no/events/courses/2020/Bergen_Phylogenetics_2020.html

ForBio travel grants
We have changed our travel grants rules. ForBio offers both incoming and outgoing travel grants to fund collaborations between ForBio members based in Norway and taxonomic experts up to NOK 14,000. Grants are given for taxonomic training with relevance to the main research project of the applicant, and aim to allow the student to do taxonomic research with specific experts, work with particular collections, or learn new preparation techniques directly from experts.  Participation in external courses, conferences, fieldwork or other kinds of activities which are not classified as expert-in-training visits are no longer eligible for support.  There are two application deadlines: March 1st 2020.

Find the detail of the reads repeats:

fq2fa ONT_A.fastq ONT_A.fasta 

minimap2 -xava-ont ONT_A.fasta ONT_A.fasta -t10 -X > AONT.paf 

awk '{if($1==$6){print}}' AONT.paf > AONTself.paf 

awk '$5=="-"' AONTself.paf | awk '{print $1}'| sort|uniq > invertedrepeat.list

Generated a few palindrome and repeats plots (highlighting only repeats largest than 10, 20 and 30 kb)

minidot -f 5 -m 30000 AONTself.paf > AONTself30000.eps 
sed 's/_template_pass_FAH31515//' AONTself30000.eps > AONTself30000final.eps 

minidot -f 5 -m 20000 AONTself.paf > AONTself20000.eps 
sed 's/_template_pass_FAH31515//' AONTself20000.eps > AONTself20000final.eps 

minidot -f 5 -m 10000 AONTself.paf > AONTself10000.eps 
sed 's/_template_pass_FAH31515//' AONTself10000.eps > AONTself10000final.eps 

Assemble with miniasm:

miniasm -f ONT_A.fasta AONT.paf > AONT.gfa 

grep '^S' AONT.gfa |awk '{print ">"$2"\n"$3}' > AONT_miniasm.fasta 

minimap2 -xasm10 AONT_miniasm.fasta AONT_miniasm.fasta -t1 -X > AONT_miniasm.paf 

awk '{if($1==$6){print}}' AONT_miniasm.paf > AONT_miniasm_self.paf 

minidot -f 5 -m 10000 AONT_miniasm_self.paf > AONT_miniasm_self10000.eps 

Njoy the assembly !

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/

./wtdbg2 -x rs -g 4.6m -t 16 -i reads.fa.gz -fo prefix
./wtpoa-cns -t 16 -i prefix.ctg.lay.gz -fo prefix.ctg.fa

Address of the bookmark: https://github.com/ruanjue/wtdbg2