Build
Description
Build a multiple sequence alignment pangraph.
Options
| Name | Type | Short Flag | Long Flag | Description |
|---|---|---|---|---|
| minimum length | Integer | l | len | minimum block size for alignment graph (in nucleotides) |
| block junction cost | Float | a | alpha | energy cost for introducing block partitions due to alignment merger |
| block diversity cost | Float | b | beta | energy cost for interblock diversity due to alignment merger |
| circular genomes | Boolean | c | circular | toggle if input genomes are circular |
| pairwise sensitivity | String | s | sensitivity | controls the pairwise genome alignment sensitivity of minimap 2. Currently only accepts "5", "10" or "20" |
| maximum self-maps | Integer | x | max-self-map | maximum number of iterations to perform block self maps per pairwise graph merger |
| enforce uppercase | Boolean | u | upper-case | toggle to force genomes to uppercase characters |
| distance calculator | String | d | distance-backend | only accepts "native" or "mash" |
| alignment kernel | String | k | alignment-kernel | only accepts "minimap2" or "mmseqs" |
| kmer length (mmseqs) | Integer | K | kmer-length | kmer length, only used for mmseqs2 alignment kernel. If not specified will use mmseqs default. |
| consistency check | Boolean | t | test | toggle to activate consistency check: verifies that input genomes can be exactly reconstructed from the graph |
| verbose mode | Boolean | v | verbose | toggle to activate verbose mode |
| debug mode | Boolean | D | debug | toggle to activate debug mode: during merging intermediate graphs are saved in the debug folder |
| random seed | Int | r | random-seed | random seed for pangraph construction. |
Arguments
Expects one or more fasta files. Multiple records within one file are treated as separate genomes Fasta files can be optionally gzipped.
Output
Prints the constructed pangraph as a JSON to stdout.