145 citations
- University of PalermoIT5 papers
- Bielefeld UniversityDE2 papers
- University of PisaIT2 papers
- Centrum Wiskunde & InformaticaNL1 paper
- Helsinki Institute for Information TechnologyFI1 paper
- Rutgers, The State University of New JerseyUS1 paper
- Universidade Federal de PernambucoBR1 paper
- University of HelsinkiFI1 paper
- Wellcome Sanger InstituteGB1 paper
8 papers
RLZAP: Relative Lempel-Ziv with Adaptive Pointers
Anthony J. Cox, Andrea Farruggia, Travis Gagie +2
Relative Lempel-Ziv (RLZ) is a popular algorithm for compressing databases of genomes from individuals of the same species when fast random access is desired. With Kuruppu et al.'s…
Lightweight LCP Construction for Very Large Collections of Strings
Anthony J. Cox, Fabio Garofalo, Giovanna Rosone +1
The longest common prefix array is a very advantageous data structure that, combined with the suffix array and the Burrows-Wheeler transform, allows to efficiently compute some com…
BEETL-fastq: a searchable compressed archive for DNA reads
Lilian Janin, Ole Schulz-Trieglaff, Anthony J. Cox
Motivation: FASTQ is a standard file format for DNA sequencing data which stores both nucleotides and quality scores. A typical sequencing study can easily generate hundreds of gig…
Lightweight LCP Construction for Next-Generation Sequencing Datasets
Markus J. Bauer, Anthony J. Cox, Giovanna Rosone +1
The advent of "next-generation" DNA sequencing (NGS) technologies has meant that collections of hundreds of millions of DNA sequences are now commonplace in bioinformatics. Knowing…
Adaptive reference-free compression of sequence quality scores
Lilian Janin, Giovanna Rosone, Anthony J. Cox
Motivation: Rapid technological progress in DNA sequencing has stimulated interest in compressing the vast datasets that are now routinely produced. Relatively little attention has…
Comparing DNA sequence collections by direct comparison of compressed text indexes
Anthony J. Cox, Tobias Jakobi, Giovanna Rosone +1
Popular sequence alignment tools such as BWA convert a reference genome to an indexing data structure based on the Burrows-Wheeler Transform (BWT), from which matches to individual…