Archives

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

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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 […]

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 […]

UNOISE2:通过对Illumina测序平台结果错误纠正进行微生物多样性分析

标题:

UNOISE2: Improved error-correction for Illumina 16S and ITS amplicon reads

摘要:

Amplicon sequencing of tags such as 16S and ITS ribosomal RNA is a popular method for investigating microbial populations. In such experiments, sequence errors caused by PCR and sequencing are difficult to distinguish from true biological variation. I describe UNOISE2, an updated version […]