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Pufferfish2

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.

The index is described in the paper Spectrum Preserving Tilings Enable Sparse and Modular Reference Indexing (RECOMB 2023).

Please, cite this paper if you use Pufferfish2.

Building and testing

Compile pufferfish2 with:

cargo build --release

Run unit and integration tests with:

cargo test

Usage: building an index

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 $\approx 1/s$ unitig and unitig occurrences, and all "popular" unitigs that occur more than <THRESH> times.

Usage: benchmarking -- querying true positive kmers

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.

Generate kmers

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

Run benchmark

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

Usage: benchmarking -- querying reads from a FASTQ file

NOTE: we currently only support pufferfish and pufferfish2 indices built with "sparse" kmer-to-unitig mappings.

Prepare reads

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

Run benchmark

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

Micro-benchmarks

Run included micro-benchmarks (via criterion) for:

  • implemented wavelet matrices

With:

cargo bench