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Centrifuge: 快速对 metagenome 序列进行分类

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Centrifuge: rapid and sensitive classification of metagenomic sequences

摘要:

Centrifuge is a novel microbial classification engine that enables rapid, accurate, and sensitive labeling of reads and quantification of species on desktop computers. The system uses an indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index, optimized specifically for the metagenomic […]

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 […]

COGNIZER: metagenome 功能注释框架

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COGNIZER: A Framework for Functional Annotation of Metagenomic Datasets

摘要:

Recent advances in sequencing technologies have resulted in an unprecedented increase in the number of metagenomes that are being sequenced world-wide. Given their volume, functional annotation of metagenomic sequence datasets requires specialized computational tools/techniques. In spite of having high accuracy, existing stand-alone functional annotation […]

RAPSearch2: 快速、高效 NGS reads 序列比对工具,无碰撞哈希表实现蛋白质序列库索引

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RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data

摘要:

Summary: With the wide application of next-generation sequencing (NGS) techniques, fast tools for protein similarity search that scale well to large query datasets and large databases are highly desirable. In a previous work, we developed RAPSearch, an algorithm that achieved […]