STAMP:基于 raw counts 、简单易用的 metagenomic communities 生物学差异鉴定工具


Identifying biologically relevant differences between metagenomic communities


Motivation: Metagenomics is the study of genetic material recovered directly from environmental samples. Taxonomic and functional differences between metagenomic samples can highlight the influence of ecological factors on patterns of microbial life in a wide range of habitats. Statistical hypothesis tests can help us distinguish ecological […]

eggNOG-mapper: COG/GO 功能注释新方案


Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper


Orthology assignment is ideally suited for functional inference. However, because predicting orthology is computationally intensive at large scale, and most pipelines relatively inaccessible, less precise homology-based functional transfer is still the default for (meta-)genome annotation. We therefore developed eggNOG-mapper, a tool for functional annotation […]



KneadData: a tool designed to perform quality control on metagenomic and metatranscriptomic sequencing data


KneadData is a tool designed to perform quality control on metagenomic sequencing data, especially data from microbiome experiments. In these experiments, samples are typically taken from a host in hopes of learning something about the microbial community on the […]

ProDeGe: 自动去除基因组序列中的污染序列


ProDeGe: a computational protocol for fully automated decontamination of genomes


Single amplified genomes and genomes assembled from metagenomes have enabled the exploration of uncultured microorganisms at an unprecedented scale. However, both these types of products are plagued by contamination. Since these genomes are now being generated in a high-throughput manner and sequences from […]