(Base Level) Degenerate String Aligner
Install cargo and rust. See the instructions here Install Rust and Cargo.
Clone and install dsa
git clone https://github.com/urbanslug/dsa.git
cd dsa
cargo install --path .
Help
dsa -h
Generate degenerate string Use https://github.com/urbanslug/simed
simed 100 > x.eds
Extract fasta MSA from .eds.
Does not extract all possible paths but only a subset of them.
dsa convert x.eds > x.msa
Split msa into multiple fasta files
./scripts/split-msa.sh x.msa
Align one of the fasta files to the eds
dsa align x.eds 0.fa > x.aln
This work is part of a project that has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 956229. Co-financed by the Connecting Europe Facility of the European Union.