Archives

Div-seq 16S 扩增子数据分析流程使用教程

重磅推出

凡通过biostack渠道购买的 USEARCH 64bit 版本,将获赠div-seq工作流。

当前USEARCH 64bit 学术/非盈利 版本价格 6600, 正规发票。

引言

微生物组研究的主要对象为特定环境中微生物群落的所有成员及其全部遗传与生理功能,传统的纯培养法经过百年来的发展和完善,从环境中分离和培养并鉴定菌株的研究工作已经接近极限,随着测序技术的发展,直接对环境样本中的保守的遗传标记片段比如:16S rRNA 基因进行扩增测序成为新的研究手段。 随着测序技术的发展以及测序成本的降低,越来越多的环境微生物多样性被研究,比如:人类肠道、温泉、土壤、火山口、南极冰川、深海、沼液、城市交通系统、生活用水等,对健康、农业、环境、海洋等重大系统问题产生深远影响。 人体微生物组计划(The Human Microbiome Project,HMP),对人体部位(胃肠道、口腔、鼻腔、女性生殖道以及皮肤)的微生物组进行广泛的研究,揭示出微生物组与人类健康状态息息相关,并推动了各国的微生物组计划和执行,美国更是将微生物组研究上升到了国家层面,提出了“国家微生物组计划”, 因此微生物研究也成为生物医学领域最火爆的前沿研究方向,未来精准医疗的重要组成部分。 为此,我们开发了div_seq 通用微生物组数据分析流程,快速有效的解析微生物的组成和功能,以便深入了解环境中微生物的群落结构及多样性和微生物的功能及代谢机理。

Div-seq 介绍

Div-seq 是完全基于 USEARCH(版本 10), USEARCH 版本10 新增了很多新的功能,包括了, 质量控制和双端序列合并 fastq_mergepairs, doi: 10.1093/bioinformatics/btv401、OTU表构建 UPARSE, Pubmed:23955772, dx.doi.org/10.1038/nmeth.2604 、 菌群组成分析 SINTAX 多样性指数分析 (alpha 和 beta)等。

流程包括了一下几个分析内容(模块):

1. 原始数据质量控制 trimming; 2. 双端序列合并 mergepairs; 3. OTU表构建 […]

Centrifuge: 快速对 metagenome 序列进行分类

标题:

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

标题:

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

标题:

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 […]

IDBA-MT: 元转录组数据拼装工具

标题:

IDBA-MT: De Novo Assembler for Metatranscriptomic Data Generated from Next-Generation Sequencing Technology

摘要:

High-throughput next-generation sequencing technology provides a great opportunity for analyzing metatranscriptomic data. However, the reads produced by these technologies are short and an assembling step is required to combine the short reads into longer contigs. As there are many repeat patterns […]

IDBA-UD: 针对单细胞以及元基因组的序列组装软件

标题:

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

摘要:

Motivation: Next-generation sequencing allows us to sequence reads from a microbial environment using single-cell sequencing or metagenomic sequencing technologies. However, both technologies suffer from the problem that sequencing depth of different regions of a genome or genomes from […]

SortmeRNA: 快速准确筛选NGS序列集合中的rRNA序列

标题:

SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data

摘要:

Motivation: The application of next-generation sequencing (NGS) technologies to RNAs directly extracted from a community of organisms yields a mixture of fragments characterizing both coding and non-coding types of RNAs. The task to distinguish among these and to further categorize the families […]

wgsim: 比较通用的序列模拟器

标题:

wgsim: Reads simulator

摘要:

Wgsim is a small tool for simulating sequence reads from a reference genome. It is able to simulate diploid genomes with SNPs and insertion/deletion (INDEL) polymorphisms, and simulate reads with uniform substitution sequencing errors. It does not generate INDEL sequencing errors, but this can be partly compensated by simulating INDEL […]

Scalpel: Indel 变异鉴定工具,支持单样本、家庭样本以及正常和肿瘤对样本

标题:

Indel variant analysis of short-read sequencing data with Scalpel.

摘要:

As the second most common type of variation in the human genome, insertions and deletions (indels) have been linked to many diseases, but the discovery of indels of more than a few bases in size from short-read sequencing data remains challenging. Scalpel (http://scalpel.sourceforge.net) is […]