生物信息常用工具集锦

过滤

SOAPnuke：华大自主开发的一款针对fastq文件的过滤软件。

HTSeq-count：一款用于reads计数的轻便软件，作者介绍说可以用于多种mapping软件的输出结果，而我则用于tophat2的输出文件做计数。不过貌似所有能转换为sam格式文件的输出都可以用htseq-count计数。

RSeQC: An RNA-seq Quality Control Package

比对

BWA：应用最为广泛的比对软件，可以比二代，也可以比三代

Soap：华大开发的比对软件，全称SOAPaligner/soap2

bowtie2：常用于RNA-seq的比对

BLASR：专门用于比对三代reads

pynast：多重序列比对软件，主要用于处理16S序列

FastTree：超快的建树软件，同时处理1M级的序列，主要用于16S的建树

数据处理

SAMtools：专门用于处理SAM、BAM格式，SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments.

Picard：a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. 

VCFtools：a program package designed for working with VCF files, such as those generated by the 1000 Genomes Project.

bcftools： utilities for variant calling and manipulating VCFs and BCFs.

bedtools：a powerful toolset for genome arithmetic, allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF.

MAKER：an easy-to-use genome annotation pipeline designed for small research groups with little bioinformatics experience.

重测序

Reseqtools：A Toolkit for analyzing next-generation DNA Re-Sequencing data. 华大内部自己整理的工具。

组装

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

SOAPdenovo

Platanus

DBG2OLC

CANU

Falcon

HGAP

变异检测 

GATK：the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. 最常用的call snp&indel 工具

BreakDancer：genome-wide detection of structural variants from next generation paired-end sequencing reads. 结构变异sv检测工具

CREST：(Clipping Reveals Structure), a new algorithm for detecting genomic structural variations at base-pair resolution using next-generation sequencing data.

CNVnator：a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads. 人重检测CNV

PennCNV：a free software tool for Copy Number Variation (CNV) detection from SNP genotyping arrays.

MIDAS：(Metagenomic Intra-species Diversity Analysis System), An integrated pipeline for estimating strain-level genomic variation from metagenomic data（可以对宏基因组 call variation）

GWAS

PLINK：whole genome association analysis toolset

SSR分析

MISA - MIcroSAtellite identification tool

SSRHunter - Simple Sequence Repeat Search tool

 

统计方法

DMM：(Dirichlet multinomial mixtures), probabilistic modelling of microbial metagenomics data.（宏基因组的概率建模）输入： frequency_matrix.csv，每行就是一个taxa，每一列都是其在每一个样本中的频率。输出：群体分析结果。The mixture components cluster communities into distinct ‘metacommunities’, and, hence, determine envirotypes or enterotypes, groups of communities with a similar composition. 该方法就是群体的PCA分析，将类似的群体归于一类。

 

RNA

cd-hit：a very widely used program for clustering and comparing protein or nucleotide sequences. 去冗余

CPAT：using logistic regression model based on 4 pure sequence-based, linguistic features. 预测RNA的编码情况

GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences. RNA比对专用

 

持续添加~