squigualiser-v0.6.3

• install via pip

python3.8 -m venv venv3
source venv3/bin/activate
pip install --upgrade pip
pip install squigualiser

• Or use the pre-compiled binary release for common Linux distributions

wget https://github.com/hiruna72/squigualiser/releases/download/v0.6.3/squigualiser-v0.6.3-linux-x86-64-binaries.tar.gz -O squigualiser.tar.gz
tar xf squigualiser.tar.gz
cd squigualiser
./squigualiser --help

• For a quick test run the following

wget https://github.com/hiruna72/squigualiser/releases/download/v0.3.0/sample_dataset.tar.gz
# or use curl
curl -L https://github.com/hiruna72/squigualiser/releases/download/v0.3.0/sample_dataset.tar.gz -o sample_dataset.tar.gz

tar xf sample_dataset.tar.gz
./squigualiser plot_pileup -f ref.fasta -s reads.blow5 -a eventalign.bam -o dir_out --region chr1:92,778,040-92,782,120 --tag_name "test_0"

• export PATH=[path_to_squigualiser_dir]:$PATH to execute squigualiser from any location.

What's Changed

• using readpaf locally by @hiruna72 in #63
• skip split reads and duplex reads

Full Changelog: v0.6.2...v0.6.3

squigualiser-v0.6.1

• install via pip

python3.8 -m venv venv3
source venv3/bin/activate
pip install --upgrade pip
pip install squigualiser

• Or use the pre-compiled binary release for common Linux distributions

wget https://github.com/hiruna72/squigualiser/releases/download/squigualiser-v0.6.1/squigualiser-v0.6.1-linux-x86-64-binaries.tar.gz -O squigualiser.tar.gz
tar xf squigualiser.tar.gz
cd squigualiser
./squigualiser --help

• For a quick test run the following

wget https://github.com/hiruna72/squigualiser/releases/download/v0.3.0/sample_dataset.tar.gz
# or use curl
curl -L https://github.com/hiruna72/squigualiser/releases/download/v0.3.0/sample_dataset.tar.gz -o sample_dataset.tar.gz

tar xf sample_dataset.tar.gz
./squigualiser plot_pileup -f ref.fasta -s reads.blow5 -a eventalign.bam -o dir_out --region chr1:92,778,040-92,782,120 --tag_name "test_0"

• export PATH=[path_to_squigualiser_dir]:$PATH to execute squigualiser from any location.

What's Changed

• add selenium to requirements by @hiruna72 in #57

Full Changelog: v0.6.0...v0.6.1

squigualiser-v0.6.0

• install via pip

python3.8 -m venv venv3
source venv3/bin/activate
pip install --upgrade pip
pip install squigualiser

• Or use the pre-compiled binary release for common Linux distributions

wget https://github.com/hiruna72/squigualiser/releases/download/v0.6.0/squigualiser-v0.6.0-linux-x86-64-binaries.tar.gz -O squigualiser.tar.gz
tar xf squigualiser.tar.gz
cd squigualiser
./squigualiser --help

• For a quick test run the following

wget https://github.com/hiruna72/squigualiser/releases/download/v0.3.0/sample_dataset.tar.gz
# or use curl
curl -L https://github.com/hiruna72/squigualiser/releases/download/v0.3.0/sample_dataset.tar.gz -o sample_dataset.tar.gz

tar xf sample_dataset.tar.gz
./squigualiser plot_pileup -f ref.fasta -s reads.blow5 -a eventalign.bam -o dir_out --region chr1:92,778,040-92,782,120 --tag_name "test_0"

• export PATH=[path_to_squigualiser_dir]:$PATH to execute squigualiser from any location.

What's Changed

• fix the link because google is sunsetting page.link in 2025 by @hasindu2008 in #51
• Dev by @hiruna72 in #54

Full Changelog: v0.5.1...v0.6.0

squigualiser-v0.5.1

• install via pip

python3.8 -m venv venv3
source venv3/bin/activate
pip install --upgrade pip
pip install squigualiser

• Or use the pre-compiled binary release for common Linux distributions

wget https://github.com/hiruna72/squigualiser/releases/download/v0.5.1/squigualiser-v0.5.1-linux-x86-64-binaries.tar.gz -O squigualiser.tar.gz
tar xf squigualiser.tar.gz
cd squigualiser
./squigualiser --help

• Or use the pre-compiled binary release for common macOS distributions

wget https://github.com/hiruna72/squigualiser/releases/download/v0.5.1/squigualiser-v0.5.1-macos-arm64-binaries.tar.gz -O squigualiser.tar.gz
# or use curl 
curl -L https://github.com/hiruna72/squigualiser/releases/download/v0.5.1/squigualiser-v0.5.1-macos-arm64-binaries.tar.gz -O squigualiser.tar.gz

tar xf squigualiser.tar.gz
cd squigualiser
./squigualiser --help

• For a quick test run the following

wget https://github.com/hiruna72/squigualiser/releases/download/v0.3.0/sample_dataset.tar.gz
# or use curl
curl -L https://github.com/hiruna72/squigualiser/releases/download/v0.3.0/sample_dataset.tar.gz -o sample_dataset.tar.gz

tar xf sample_dataset.tar.gz
./squigualiser plot_pileup -f ref.fasta -s reads.blow5 -a eventalign.bam -o dir_out --region chr1:92,778,040-92,782,120 --tag_name "test_0"

• export PATH=[path_to_squigualiser_dir]:$PATH to execute squigualiser from any location.

squigualiser-v0.5.0

• install via pip

python3.8 -m venv venv3
source venv3/bin/activate
pip install --upgrade pip
pip install squigualiser

• Or use the pre-compiled binary release for common Linux distributions

wget https://github.com/hiruna72/squigualiser/releases/download/v0.5.0/squigualiser-v0.5.0-linux-x86-64-binaries.tar.gz -O squigualiser.tar.gz
tar xf squigualiser.tar.gz
cd squigualiser
./squigualiser --help

• Or use the pre-compiled binary release for common macOS distributions

wget https://github.com/hiruna72/squigualiser/releases/download/v0.5.0/squigualiser-v0.5.0-macos-arm64-binaries.tar.gz -O squigualiser.tar.gz
# or use curl 
curl -L https://github.com/hiruna72/squigualiser/releases/download/v0.5.0/squigualiser-v0.5.0-macos-arm64-binaries.tar.gz -O squigualiser.tar.gz

tar xf squigualiser.tar.gz
cd squigualiser
./squigualiser --help

• For a quick test run the following

wget https://github.com/hiruna72/squigualiser/releases/download/v0.3.0/sample_dataset.tar.gz
# or use curl
curl -L https://github.com/hiruna72/squigualiser/releases/download/v0.3.0/sample_dataset.tar.gz -o sample_dataset.tar.gz

tar xf sample_dataset.tar.gz
./squigualiser plot_pileup -f ref.fasta -s reads.blow5 -a eventalign.bam -o dir_out --region chr1:92,778,040-92,782,120 --tag_name "test_0"

• export PATH=[path_to_squigualiser_dir]:$PATH to execute squigualiser from any location.

squigualiser-v0.4.0-beta

• pip package added.

python3.8 -m venv venv3
source venv3/bin/activate
pip install --upgrade pip
pip install squigualiser==0.4.0b0

squigualiser-v0.3.0

• install via pip

python3.8 -m venv venv3
source venv3/bin/activate
pip install --upgrade pip
pip install squigualiser

• Or use the pre-compiled binary release for common Linux distributions

wget https://github.com/hiruna72/squigualiser/releases/download/v0.3.0/squigualiser-v0.3.0-linux-x86-64-binaries.tar.gz -O squigualiser.tar.gz
tar xf squigualiser.tar.gz
cd squigualiser
./squigualiser --help

• Or use the pre-compiled binary release for common macOS distributions

wget https://github.com/hiruna72/squigualiser/releases/download/v0.3.0/squigualiser-v0.3.0-macos-arm64-binaries.tar.gz -O squigualiser.tar.gz
# or use curl 
curl -L https://github.com/hiruna72/squigualiser/releases/download/v0.3.0/squigualiser-v0.3.0-macos-arm64-binaries.tar.gz -O squigualiser.tar.gz

tar xf squigualiser.tar.gz
cd squigualiser
./squigualiser --help

• For a quick test run the following

wget https://github.com/hiruna72/squigualiser/releases/download/v0.3.0/sample_dataset.tar.gz
# or use curl
curl -L https://github.com/hiruna72/squigualiser/releases/download/v0.3.0/sample_dataset.tar.gz -o sample_dataset.tar.gz

tar xf sample_dataset.tar.gz
./squigualiser plot_pileup -f ref.fasta -s reads.blow5 -a eventalign.bam -o dir_out --region chr1:92,778,040-92,782,120 --tag_name "test_0"

• export PATH=[path_to_squigualiser_dir]:$PATH to execute squigualiser from any location.

squigualiser-v0.3.0-beta

• pip package added.

python3.8 -m venv venv3
source venv3/bin/activate
pip install --upgrade pip
pip install squigualiser==0.3.0b0

squigualiser-v0.2.0

• Pileup view functionality.
• GUI support through a web app functionality.
• Bed annotation support.
• More documentation.

https://twitter.com/hiruna72/status/1669594790391078912

squigualiser-v0.1.0-alpha

Introducing squigualiser, a powerful toolkit for visualising nanopore raw signals.
https://twitter.com/hiruna72/status/1640482307068035073