Genome sequencing and analysis allow researchers to decode the functional information
hidden in DNA sequences as well as to study cell to cell variation within a cell population …

Abstract The Sequence Alignment/Map (SAM) format file is the text file used to record
alignment information. Alignment is the core of sequencing analysis, and downstream tasks …

The last two decades have witnessed a dramatic increase in the amount of highly repetitive
datasets consisting of sequential data (strings, texts). Processing these massive amounts of …

Given the popularity and elegance of k-mer-based tools, finding a space-efficient way to
represent a set of k-mers is important for improving the scalability of bioinformatics analyses …

Background The increasing production of genomic data has led to an intensified need for
models that can cope efficiently with the lossless compression of DNA sequences. Important …

Metagenomics is a rapidly expanding field that uses next-generation sequencing technology
to analyze the genetic makeup of environmental samples. However, accurately identifying …

K-mer based methods have become prevalent in many areas of bioinformatics. In
applications such as database search, they often work with large multi-terabyte-sized …

Background Advances in sequencing technologies have enabled the characterization of
multiple microbial and host genomes, opening new frontiers of knowledge while kindling …

Background Nearly all molecular sequence databases currently use gzip for data
compression. Ongoing rapid accumulation of stored data calls for a more efficient …

Real-world data often comes in compressed form. Analyzing compressed data directly
(without first decompressing it) can save space and time by orders of magnitude. In this …