Related papers: Engineering Relative Compression of Genomes
With current hardware and software, a standard computer can now hold in RAM an index for approximate pattern matching on about half a dozen human genomes. Sequencing technologies have improved so quickly, however, that scientists will soon…
Given a static reference string $R$ and a source string $S$, a relative compression of $S$ with respect to $R$ is an encoding of $S$ as a sequence of references to substrings of $R$. Relative compression schemes are a classic model of…
While achieving a compression ratio of 2.0 bits/base, the new algorithm codes non-N bases in fixed length. It dramatically reduces the time of coding and decoding than previous DNA compression algorithms and some universal compression…
We present RCT, a new compact data structure to represent trajectories of objects. It is based on a relative compression technique called Relative Lempel-Ziv (RLZ), which compresses sequences by applying an LZ77 encoding with respect to an…
Motivation The Burrows-Wheeler transform (BWT) is the foundation of many algorithms for compression and indexing of text data, but the cost of computing the BWT of very large string collections has prevented these techniques from being…
Recent studies in DNA sequence classification have leveraged sophisticated machine learning techniques, achieving notable accuracy in categorizing complex genomic data. Among these, methods such as k-mer counting have proven effective in…
Genome sequence analysis, which examines the DNA sequences of organisms, drives advances in many critical medical and biotechnological fields. Given its importance and the exponentially growing volumes of genomic sequence data, there are…
Advances in DNA sequencing mean databases of thousands of human genomes will soon be commonplace. In this paper we introduce a simple technique for reducing the size of conventional indexes on such highly repetitive texts. Given upper…
From a long time ago, beside encryption of data and making it secure, compression packing it was also important that could make transmission of data faster. In the past years need for improvement of encryption and compression for a fast and…
Motivation: High-coverage sequencing data have significant, yet hard to exploit, redundancy. Most FASTQ compressors cannot efficiently compress the DNA stream of large datasets, since the redundancy between overlapping reads cannot be…
We present a simple adaptation of the Lempel Ziv 78' (LZ78) compression scheme ({\em IEEE Transactions on Information Theory, 1978}) that supports efficient random access to the input string. Namely, given query access to the compressed…
Suffix trees are one of the most versatile data structures in stringology, with many applications in bioinformatics. Their main drawback is their size, which can be tens of times larger than the input sequence. Much effort has been put into…
The paper introduces a new lossless, highly robust compression algorithm that similar with LZW algorithm, yet the algorithm discards dictionary processing and uses irregular sequences with massive, random information instead. Then the paper…
Lempel-Ziv-Double (LZD) is a variation of the LZ78 compression scheme that achieves better compression on repetitive datasets. Nevertheless, prior research has identified computational inefficiencies and a weakness in its compressibility…
Grammar-based compression is a popular and powerful approach to compressing repetitive texts but until recently its relatively poor time-space trade-offs during real-life construction made it impractical for truly massive datasets such as…
Minimizing data storage poses a significant challenge in large-scale metagenomic projects. In this paper, we present a new method for improving the encoding of FASTQ files generated by metagenomic sequencing. This method incorporates…
In the field of biological research, it is essential to comprehend the characteristics and functions of molecular sequences. The classification of molecular sequences has seen widespread use of neural network-based techniques. Despite their…
We raise the question of approximating the compressibility of a string with respect to a fixed compression scheme, in sublinear time. We study this question in detail for two popular lossless compression schemes: run-length encoding (RLE)…
We describe a grammar for DNA sequencing reads from which we can compute the BWT directly. Our motivation is to perform in succinct space genomic analyses that require complex string queries not yet supported by repetition-based…
DNA has emerged as a promising alternative for long-term data storage due to its high capacity, durability, and low-energy potential. However, storing data in DNA presents several challenges. First, it requires complex and costly…