過濾
SOAPnuke：華大自主開發的一款針對fastq文件的過濾軟件。
HTSeq-count：一款用於reads計數的輕便軟件，作者介紹說可以用於多種mapping軟件的輸出結果，而我則用於tophat2的輸出文件做計數。不過貌似所有能轉換為sam格式文件的輸出都可以用htseq-count計數。
RSeQC: An RNA-seq Quality Control Package
比對
BWA：應用最為廣泛的比對軟件，可以比二代，也可以比三代
Soap：華大開發的比對軟件，全稱SOAPaligner/soap2
bowtie2：常用於RNA-seq的比對
BLASR：專門用於比對三代reads
pynast：多重序列比對軟件，主要用於處理16S序列
FastTree：超快的建樹軟件，同時處理1M級的序列，主要用於16S的建樹
數據處理
SAMtools：專門用於處理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.
重測序
Reseqtools：A Toolkit for analyzing next-generation DNA Re-Sequencing data. 華大內部自己整理的工具。
組裝
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
SOAPdenovo
Platanus
DBG2OLC
CANU
Falcon
HGAP
變異檢測
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. 結構變異sv檢測工具
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. 人重檢測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（可以對宏基因組 call variation）
GWAS
PLINK：whole genome association analysis toolset
SSR分析
MISA - MIcroSAtellite identification tool
SSRHunter - Simple Sequence Repeat Search tool
統計方法
DMM：(Dirichlet multinomial mixtures), probabilistic modelling of microbial metagenomics data.（宏基因組的概率建模）輸入： frequency_matrix.csv，每行就是一個taxa，每一列都是其在每一個樣本中的頻率。輸出：群體分析結果。The mixture components cluster communities into distinct ‘metacommunities’, and, hence, determine envirotypes or enterotypes, groups of communities with a similar composition. 該方法就是群體的PCA分析，將類似的群體歸於一類。
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. 預測RNA的編碼情況
GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences. RNA比對專用
持續添加~