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

标题:

Identifying biologically relevant differences between metagenomic communities

摘要:

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

标题:

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

摘要:

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:微生物组实验质量控制

标题:

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

摘要:

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

文章标题:

ProDeGe: a computational protocol for fully automated decontamination of genomes

文章摘要:

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 […]