A command line interface for the sbwt crate. To compile, run cargo build -r. Then, run ./target/release/sbwt for instructions. At the time of writing this README.md, the CLI provides the following subcommands:
Command line tools using for the sbwt library.
Usage: sbwt [OPTIONS] [COMMAND]
Commands:
build Build the SBWT and possibly the LCS array
merge Merge two SBWT indexes
build-lcs Build the LCS array given an existing SBWT. Note that it's also possible build the SBWT and the LCS at the same time with the build-command.
benchmark Benchmark queries on the index
lookup Look up the colex ranks of all k-mers. Printed as space-separated ascii integers, one line per query sequence. If a k-mer does not exist in the index, the colex rank is -1.
matching-statistics
jaccard Compute the Jaccard index of the k-mer sets in two given sbwt index files.
dump-kmers Prints all k-mer strings in colex order, one per line.
dump-unitigs Print all unitigs in arbitrary order in FASTA format
help Print this message or the help of the given subcommand(s)
Options:
-t, --threads <threads> Number of threads to use for parallelized operations [default: 4]
-v, --verbose Print more information when running.
-h, --help Print help