Pufferfish2
is a reference based index for exact k-mer queries designed to be a successor to
Pufferfish
.
Pufferfish2
sparsifies and compresses a pufferfish
index by sampling unitigs and corresponding unitig-occurrences stored in pufferfish
's "unitig table", utab
.
Currently, pufferfish2
is also minimal reimplementation of pufferfish
providing load-only compatibility.
Compile pufferfish2
with:
cargo build --release
Run unit and integration tests with:
cargo test
After building a pufferfish
index, build a pufferfish2
index with:
usage: sparsify_ctg_table [OPTIONS] --index-dir <INDEX_DIR> --out-index-dir <OUT_INDEX_DIR> <COMMAND>
Commands:
strided-bv-pop
Options:
-i, --index-dir <INDEX_DIR>
-o, --out-index-dir <OUT_INDEX_DIR>
-s, --sampled-wm-thresh <SAMPLED_WM_THRESH> [default: 64]
-n, --nonsamp-wm-thresh <NONSAMP_WM_THRESH> [default: 64]
-h, --help Print help information
-V, --version Print version information
With subcommand: strided-bv-pop --stride --thresh
Options:
-s, --stride <STRIDE>
-t, --thresh <THRESH>
-h, --help Print help information
That samples positions of <THRESH>
times.
NOTE: we currently only support pufferfish
and pufferfish2
indices built with "sparse" kmer-to-unitig mappings.
The provided benchmarking binaries first prepares input data and saves inputs to disks for repeatability and to avoid I/O bounds.
First generate k-mers from an existing sparse pufferfish
index by pointing the binary to the directory containing a pufferfish
index.
Usage: bench gen-kmers [OPTIONS] --input --output --n-kmers <N_KMERS>
Options:
-i, --input <INPUT>
-o, --output <OUTPUT>
-n, --n-kmers <N_KMERS>
-k, --k <K> [default: 31]
-s, --seed <SEED> [default: 290348]
-h, --help Print help information
-V, --version Print version information
Provide <INPUT_KMERS>
generated kmer set, then provide to pufferfish
or pufferfish2
variants via <COMMAND>
.
New pufferfish2
indices using dense and sparse kmer-to-unitig mappings should be provided with sparse-dense
and sparse-sparse
commands, respectively. Old pufferfish
variants using dense and sparse kmer-to-unitig mappings should be provided with dense
and sparse
commands, respectively.
Usage: bench kmers [OPTIONS] --input-kmers <INPUT_KMERS> <COMMAND>
Commands:
sparse-sparse
sparse-dense
dense
sparse
help Print this message or the help of the given subcommand(s)
Options:
-i, --input-kmers <INPUT_KMERS>
-k, --k <K> [default: 31]
-n, --n-kmers <N_KMERS>
-h, --help Print help information
-V, --version Print version information
NOTE: we currently only support pufferfish
and pufferfish2
indices built with "sparse" kmer-to-unitig mappings.
Provide <INPUT>
prepared readset, then provide to pufferfish
or pufferfish2
variants via <COMMAND>
.
First load and prepare <MAX_RADS>
reads from an input .fastq
or .fastq.gz
file --- prep-fastq
processes and stores 2-bit encoded reads to disk.
Usage: bench prep-fastq [OPTIONS] --input <INPUT> --output <OUTPUT>
Options:
-i, --input <INPUT>
-m, --max-reads <MAX_READS>
-o, --output <OUTPUT>
-h, --help Print help information
-V, --version Print version information
Provide <INPUT>
prepared readset, then provide to pufferfish
or pufferfish2
variants via <COMMAND>
.
New pufferfish2
indices using dense and sparse kmer-to-unitig mappings should be provided with sparse-dense
and sparse-sparse
commands, respectively. Old pufferfish
variants using dense and sparse kmer-to-unitig mappings should be provided with dense
and sparse
commands, respectively.
Usage: bench readset --input <INPUT> <COMMAND>
Commands:
sparse-sparse
sparse-dense
dense
sparse
help Print this message or the help of the given subcommand(s)
Options:
-i, --input <INPUT>
-h, --help Print help information
-V, --version Print version information
Run included micro-benchmarks (via criterion
) for:
- implemented wavelet matrices
With:
cargo bench