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 …

… Breitwieser … For more details on competing paradigms for read classification, see
Breitwieser et al. … $ bowtie2 -x bowtie_index/GRCh38 -p 8 -f -1 paired_reads_1.fastq \ -2 …

… It then replaces these three species with the genus, thereby reducing the number of
assignments to four (genus I plus species D, E, and F). If more than five taxonomic labels had …

Metagenomic experiments attempt to characterize microbial communities using high-throughput
DNA sequencing. Identification of the microorganisms in a sample provides information …

Pavian is a web application for exploring classification results from metagenomics experiments.
With Pavian, researchers can analyze, visualize and transform results from various …

False-positive identifications are a significant problem in metagenomics classification. We
present KrakenUniq, a novel metagenomics classifier that combines the fast k-mer-based …

We assembled the sequences from deep RNA sequencing experiments by the Genotype-Tissue
Expression (GTEx) project, to create a new catalog of human genes and transcripts, …

MMseqs2 taxonomy is a new tool to assign taxonomic labels to metagenomic contigs. It extracts
all possible protein fragments from each contig, quickly retains those that can contribute …

Objective: To determine the feasibility of next-generation sequencing (NGS) microbiome
approaches in the diagnosis of infectious disorders in brain or spinal cord biopsies in patients …

Contaminant sequences that appear in published genomes can cause numerous problems
for downstream analyses, particularly for evolutionary studies and metagenomics projects. …