Softwares - pseudogene/aquaexcel GitHub Wiki

Clients (for students)

Windows users

• MobaXterm: Enhanced terminal for Windows - Download
• Filezilla client for supports FTP, and SFTP upload/download - Download
• Integrative Genomics Viewer (IGV) high-performance visualization tool for interactive exploration of large, integrated genomic datasets - Download

Mac users

• Filezilla client for supports FTP, and SFTP upload/download - Download
• Integrative Genomics Viewer (IGV) high-performance visualization tool for interactive exploration of large, integrated genomic datasets - Download

Servers (for teachers)

Sequence quality

• fastqc

Unspliced and spliced sequence alignments

• trim galore
• bwa
• minimap2
• hisat2
• samtools
• Picard

Variation calling

• freebayes

RNA-Seq expression measurement

• RSEM
• subread

Genome assembly with short and long reads

• spades
• miniasm
• wtdbg2
• racon
• pilon

16S analyses

• mothur
• Krona

GBS/Rad

• stacks

Cloud access

AMI

Full installation

Based on a clean distribution of Ubuntu 19.04

apt update
apt install -y gcc cmake
apt install -y bwa hisat2 samtools freebayes spades miniasm rsem fastqc cutadapt mothur vsearch
apt-get install -y python-pip autoconf automake make g++ libz-dev

curl -fsSL https://github.com/FelixKrueger/TrimGalore/archive/0.6.0.tar.gz -o trim_galore.tar.gz
tar xzf trim_galore.tar.gz
cp TrimGalore-0.6.0/trim_galore /usr/local/bin/
rm -rf trim_galore.tar.gz TrimGalore-0.6.0/

curl -fsSL https://github.com/broadinstitute/pilon/releases/download/v1.23/pilon-1.23.jar -o pilon.jar
mv pilon.jar /usr/local/bin/
#java -Xmx16G -jar /usr/local/bin/pilon.jar

curl -fsSL https://github.com/broadinstitute/picard/releases/download/2.20.5/picard.jar -o picard.jar
mv picard.jar /usr/local/bin/
#java -Xmx16G -jar /usr/local/bin/picard.jar

curl -fsSL https://github.com/isovic/racon/releases/download/1.4.3/racon-v1.4.3.tar.gz -o racon-v1.4.3.tar.gz
tar xzf racon-v1.4.3.tar.gz
cd racon-v1.4.3
cmake -DCMAKE_BUILD_TYPE=Release
make
make install
cd ..
rm -rf racon-v1.4.3.tar.gz racon-v1.4.3/

curl -L https://github.com/lh3/minimap2/releases/download/v2.17/minimap2-2.17_x64-linux.tar.bz2 | tar -jxvf -
cp minimap2-2.17_x64-linux/minimap2 /usr/local/bin/
rm -rf minimap2-2.17_x64-linux

curl -fsSL https://github.com/ruanjue/wtdbg2/releases/download/v2.4/wtdbg-2.4_x64_linux.tar.gz -o wtdbg-2.4_x64_linux.tar.gz
tar xzf wtdbg-2.4_x64_linux.tar.gz
cp wtdbg-2.4_x64_linux/* /usr/local/bin/
cp wtdbg-2.4_x64_linux/scripts/* /usr/local/bin/
rm -rf wtdbg-2.4_x64_linux.tar.gz wtdbg-2.4_x64_linux

curl -fsSL https://sourceforge.net/projects/subread/files/subread-1.6.5/subread-1.6.5-Linux-x86_64.tar.gz/download -o subread-1.6.5-Linux-x86_64.tar.gz
tar xzf subread-1.6.5-Linux-x86_64.tar.gz
cp subread-1.6.5-Linux-x86_64/bin/utilities/* /usr/local/bin/
cp subread-1.6.5-Linux-x86_64/bin/* /usr/local/bin/
rm -rf subread-1.6.5-Linux-x86_64.tar.gz subread-1.6.5-Linux-x86_64

curl -fsSL https://github.com/marbl/Krona/archive/v2.7.1.tar.gz -o v2.7.1.tar.gz
tar xfz v2.7.1.tar.gz 
cd Krona-2.7.1/KronaTools
./install.pl
cd ../..
rm -rf v2.7.1.tar.gz Krona-2.7.1

curl https://raw.githubusercontent.com/accaldwell/mothur_krona/master/mothur_krona_XML.py > /usr/local/bin/mothur_krona_XML.py
chmod 755 /usr/local/bin/mothur_krona_XML.py
pip install lxml

curl -fsSL http://catchenlab.life.illinois.edu/stacks/source/stacks-2.41.tar.gz -o stacks-2.41.tar.gz
tar xfz stacks-2.41.tar.gz
cd stacks-2.41
./configure
make -j 8
make install
cd ..
rm -rf stacks-2.41.tar.gz stacks-2.41