Genomic structure frequency estimation from genome assembly graphs and long reads.
Install dependencies using conda. I recommend using the mamba version of conda.
mamba create -n traversome_env
mamba activate traversome_env
mamba install -c bioconda graphaligner python numpy scipy sympy python-symengine dill typer loguru pyyaml gekkoInstall Traversome using pip.
git clone --depth=1 https://github.com/JianjunJin/Traversome
pip install ./Traversome --no-depstraversome thorough -g graph.gfa -a align.gaf -o outdir --topo circularImportant optional flags to finetune for achieving valid result (high bootstrap support):
--min-read-id Threshold for alignment identity, read with below which the alignment will be discarded. [default: 0.992]
--min-record-id Threshold for alignment identity, a record of a read with below which the alignment will be discarded. [default: 0.99]
--min-align-len Threshold for the continuous alignment length of a read, below which the alignment will be discarded. [default: 5000]
--min-align-counts Threshold for counts per path, below which the alignment(s) of that path will be discarded. The default automatic selection (-1) does not guarantee the best performance - good bootstrap support. [default: auto]
Use traversome thorough -h to see details for above flags and other flags.
|-- output_dir
|-- traversome.log.txt running log
|-- variants.info.tab information of survival variants after model selection and bootstrap
|-- bootstrap.replicates.tab bootstrap results
|-- final.result.tab summary of pangenome solutions
|-- variant.*.fasta sequence of each variant in the best supported result
|-- pangenome.gfa pangenome graph of the best supported result
|-- options.yaml information of options
|-- readpath.info.tab read path index -> compatible variants and number of supported reads
|-- readpath.unused.info.tab filtered-out-unused read path index -> compatible variants and number of supported reads
|-- readpath.record_ids.tab information of read paths and their congruent variant