PFP-eBWT

PFP-eBWT is a tool that computes the eBWT of string collections using the Prefix-Free Parsing method (PFP).

Usage

Construction of the eBWT:

usage: pfpebwt [-h] [-w WSIZE] [-p MOD] [-t T] [-n N] [-r] [-v] [-d] [--reads]
               [--period] [--invert] [--keep] [--parsing]
               input

positional arguments:
  input                 input fasta file name

optional arguments:
  -h, --help            show this help message and exit
  -w WSIZE, --wsize WSIZE
                        sliding window size (def. 10)
  -p MOD, --mod MOD     hash modulus (def. 100)
  -t T                  number of helper threads (def. None)
  -n N                  number of different primes (def. 2)
  -r                    store the eBWT in RLE format (def. False)
  -v                    verbose (def. False)
  -d                    use different remainders instead of different prime numbers (def. False)
  --reads               process input as a read collection (def. False)
  --period              remove sequences which are not primitive (def. False)
  --invert              invert the eBWT (def. False)
  --keep                keep auxiliary files (debug only)
  --parsing             stop after the parsing phase (debug only)

The default algorithm will run with one prime number and one remainder to search for the trigger strings. If you want to build the eBWT of a collection of short sequences you have to use the --reads flag, and set with -n the maximum number of different primes allowed. With -d you can use different remainders instead of different primes. You can activate the --period flag in case your dataset contains non-primitive words, this flag will allow to filter them out. You can activate the --invert flag in case you want to invert the eBWT and write the inverted sequences to a file, this process requires to compute the WT of the eBWT in the internal memory.

Example

Download and Compile

git clone https://github.com/davidecenzato/PFP-eBWT.git
cd PFP-eBWT
mkdir build
cd build
cmake ..
make

Run on Example Data

// Build the eBWT on a toy data set
python3 pfpebwt yeast.fasta -w 10 -p 100 

External resources

• gSACA-K
• malloc_count
• sdsl-lite

Citation

Please, if you use this tool in an academic setting cite the following paper:

PFP-eBWT

@inproceedings{BoucherCL0S21a,
  author    = {Christina Boucher and
               Davide Cenzato and
               Zsuzsanna Lipt{\'{a}}k and
               Massimiliano Rossi and
               Marinella Sciortino},
  title     = {Computing the Original e{BWT} Faster, Simpler, and with Less Memory},
  booktitle = {Proceedings of 28th International Symposium in String Processing and Information Retrieval {SPIRE} 2021},
  series    = {Lecture Notes in Computer Science},
  volume    = {12944},
  pages     = {129--142},
  year      = {2021}
}

Authors

Theoretical results:

• Christina Boucher
• Davide Cenzato
• Zsuzsanna Lipták
• Massimiliano Rossi
• Marinella Sciortino

Implementation and experiments:

• Davide Cenzato
• Massimiliano Rossi

References

[1] Christina Boucher, Travis Gagie, Alan Kuhnle and Giovanni Manzini: Prefix-Free Parsing for Building Big BWTs. In Proc. of the 18th International Workshop on Algorithms in Bioinformatics, WABI 2018.

[2] Christina Boucher, Travis Gagie, Alan Kuhnle, Ben Langmead, Giovanni Manzini and Taher Mun: Prefix-free parsing for building big BWTs. Algorithms Mol. Biol. 14(1): 13:1-13:15 (2019)

[3] Ge Nong, Sen Zhang and Wai Hong Chan: Two Efficient Algorithms for Linear Time Suffix Array Construction. IEEE Trans. Computers 60(10): 1471-1484 (2011)

[4] Hideo Bannai, Juha Kärkkäinen, Dominik Köppl and Marcin Piatkowski: Constructing the bijective and the extended Burrows-Wheeler-Transform in linear time. In Proc. of the 32nd Annual Symposium on Combinatorial Pattern Matching, CPM 2021.