Microbiome research has grown rapidly over the past decade, with a proliferation of new
methods that seek to make sense of large, complex data sets. Here, we survey two of the …

It has been over a decade since the first publication of a method dedicated entirely to
mapping long-reads. The distinctive characteristics of long reads resulted in methods …

Although Kraken'sk-mer-based approach provides a fast taxonomic classification of
metagenomic sequence data, its large memory requirements can be limiting for some …

k-mer-based methods are widely used in bioinformatics for various types of sequence
comparisons. However, a single mutation will mutate k consecutive k-mers and make most k …

High-throughput sequencing (HTS) is increasingly being used for broad applications of
microbial char-acterization, such as microbial ecology, clinical diagnosis, and outbreak …

Genome search and/or classification typically involves finding the best-match database
(reference) genomes and has become increasingly challenging due to the growing number …

Targeted metagenomics, also known as metagenetics, is a high-throughput sequencing
application focusing on a nucleotide target in a microbiome to describe its taxonomic …

Motivation The growing number of microbial reference genomes enables the improvement
of metagenomic profiling accuracy but also imposes greater requirements on the indexing …

Background Large scale metagenomic projects aim to extract biodiversity knowledge
between different environmental conditions. Current methods for comparing microbial …

Processing large data sets has become an essential part of computational genomics.
Greatly increased availability of sequence data from multiple sources has fueled …