Important Software

• here i include a few basic programs that are Important
• this list is not complete, because it changes usually quite fast

SRA-toolkit

• link to sra website

wget https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/current/sratoolkit.current-ubuntu64.tar.gz
tar xf sratoolkit.current-ubuntu64.tar.gz
cd sratoolkit.2.8.2-1-ubuntu64/bin
mv * ~/.local/bin

Assembly-stats

• for installation see github

porechop

• Adapter removal and demultiplexing of nanopore data
• for installation see github

minimap2 & miniasm

• fast but error-prone long read assembler

Use this only with pilon and Illumina correction

• github link minimap2
• github link miniasm

# Install minimap and miniasm (requiring gcc and zlib)
git clone https://github.com/lh3/minimap && (cd minimap && make)
git clone https://github.com/lh3/miniasm && (cd miniasm && make)

MUMmer

• github link

wget https://github.com/mummer4/mummer/releases/download/v4.0.0beta2/mummer-4.0.0beta2.tar.gz
tar xf mummer-4.0.0beta2.tar.gz
cd mummer-4.0.0beta2/
./configure LDFLAGS=-static
make
sudo make install

Unicycler

• Hybrid assembler pipeline
• github link