fastq格式相关
SRAtoolkit
SRA数据库下载公用数据时的工具
网址 https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc
fastx toolkit
a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing
有各种各样的小功能，比如提取反向互补序列等等。
网址 http://hannonlab.cshl.edu/fastx_toolkit/
fastqc
A quality control tool for high throughput sequence data
评估测序数据质量
网址 https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
MultQC
Aggregate results from bioinformatics analyses across many samples into a single report
一次同时生成多个数据质量报告，省时省力方便对比，支持fastqc
网址 https://github.com/ewels/MultiQC
网址 http://multiqc.info/docs/
Trim Galore
around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries
和fastqc出自一家，可以和fastqc结合使用，用来清洗原始数据。
网址 https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
Trimmomatic
A flexible read trimming tool for Illumina NGS data
专门清洗illumina测序数据的工具
网址 http://www.usadellab.org/cms/index.php?page=trimmomatic
khmer
working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells.
可以对原始测序数据进行过滤等
网址 http://khmer.readthedocs.io/en/v2.1.1/user/scripts.htm
BED格式相关
bedops
the fast, highly scalable and easily-parallelizable genome analysis toolkit
网址 https://bedops.readthedocs.io/en/latest/index.html
玩转bed格式文件，速度比bedtools快
bedtools
a powerful toolset for genome arithmetic
网址 http://bedtools.readthedocs.io/en/latest/index.html
最知名的bed文件相关工具，但是和samtools并非出自一家
SAM/BAM格式相关
samtools
Utilities for the Sequence Alignment/Map (SAM) format
网址 http://www.htslib.org/doc/samtools.html
有这一个就够了
SNP（VCF/BCF）相关
GATK
网址 https://software.broadinstitute.org/gatk/documentation/
使用率最高的软件
bcftools
utilities for variant calling and manipulating VCFs and BCFs
网址 http://www.htslib.org/doc/bcftools.html
对vcf格式的文件进行各种操作
vcftools
网址 https://vcftools.github.io/man_latest.html
和bcftools类似
snpEFF
Genetic variant annotation and effect prediction toolbox
适合用来进行snp注释
用法 http://snpeff.sourceforge.net/SnpEff_manual.html
网址 http://snpeff.sourceforge.net/
也可以注释ChIP-seq
支持非编码注释，如组蛋白修饰
samtools mpileup
Utilities for the Sequence Alignment/Map (SAM) format
网址 http://www.htslib.org/doc/samtools.html
ChIP-seq/motif
MACS
Model-based Analysis of ChIP-Seq
主要用于组蛋白修饰产生的narrow peaks(H3K4me3 and H3K9/27ac)
transcription factors which are usually associated with sharp and solated peaks
网址 http://liulab.dfci.harvard.edu/MACS/README.html
MACS2
网址 https://github.com/taoliu/MACS
MACS的升级版本，也可以用来找broad peak
SICER
highly recommended for a practical ChIP-seq experiment design and can be used to account for local biases resulting from read mappability, DNA repeats, local GC content
网址https://www.genomatix.de/online_help/help_regionminer/sicer.html
出来怼MACS，主要用来找一些比较宽的peak,类似于H3K9me3 和 H3K36me3。
large sequences alignment
长序列比对常用的几个软件
MUMer
rapid alignment of very large DNA and amino acid sequences
网址 http://mummer.sourceforge.net/examples/
网址 http://mummer.sourceforge.net/manual/
GMAP
GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences
网址 http://research-pub.gene.com/gmap/
BLAT
Blat produces two major classes of alignments:at the DNA level between two sequences that are of 95% or greater identity, but which may include large inserts；at the protein or translated DNA level between sequences that are of 80% or greater identity and may also include large inserts.
网址 https://genome.ucsc.edu/goldenpath/help/blatSpec.html
short reads alignment
短序列比对，二代测序数据比对
BWA
Burrows-Wheeler Alignment Tool
mapping low-divergent sequences against a large reference genome
It consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM.
网址 http://bio-bwa.sourceforge.net/bwa.shtml
网址 https://github.com/lh3/bwa
GSNAP
Genomic Short-read Nucleotide Alignment Program
网址 http://research-pub.gene.com/gmap/
Bowtie
works best when aligning short reads to large genomes
not yet report gapped alignments
网址 http://bowtie-bio.sourceforge.net/manual.shtml
Bowtie2
ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences
supports gapped, local, and paired-end alignment modes
网址 http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#reporting
和上一代的区别在于支持gapped alignments
HISAT2
Tophat的继任者，基于HISAT和Bowtie2
HISAT2的速度比STAR快一些
网址 http://ccb.jhu.edu/software/hisat2/manual.shtml
STAR
Spliced Transcripts Alignment to a Reference
网址 https://github.com/alexdobin/STAR
网址 https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf
genome guide assemble
stringtie
highly efficient assembler of RNA-Seq alignments into potential transcripts
对于可变剪切的发现相对准确
网址 https://ccb.jhu.edu/software/stringtie/
Cufflinks
基本不用了。。。
IDP
Isoform Detection and Prediction tool
gmap+hisat2,也就是长短序列比对相结合，效果不错
网址 https://www.healthcare.uiowa.edu/labs/au/IDP/IDP_manual.asp
de novo assemble/gene prediction
下面几个软件结合起来就是一个从组装到注释到计算效率的过程
trintiy
倾向于预测长的可变剪接
新版本从之前的过度预测越来越倾向于有所保留
比较耗资源，一般1个CPU最好分配6G-10G
可以有参或者无参转录组拼接
网址 https://github.com/trinityrnaseq/trinityrnaseq/wiki
oases
通常得到的N50比较高
检测低表达的基因有一定优势
De novo transcriptome assembler for very short reads
网址 https://github.com/dzerbino/oases
PASA（内包括BLAT和GMAP）
得到拼接好的fasta文件后可以用pasa进行基因结构预测
Gene Structure Annotation and Analysis Using PASA
网址 http://pasapipeline.github.io/
Maker
基因预测
can be used for de novo annotation of newly sequenced genomes, for updating existing annotations to reflect new evidence, or just to combine annotations, evidence, and quality control statistics
网址 http://www.yandell-lab.org/software/maker.html
TransRate
reference free quality assessment of de novo transcriptome assemblies
网址 http://hibberdlab.com/transrate/
专业的拼接质量评估软件，有三种评估模式。
DETONATE
DE novo TranscriptOme rNa-seq Assembly with or without the Truth Evaluation
网址 https://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0553-5
BUSCO
它的评估模式和上面两个不太一样
based on evolutionarily-informed expectations of gene content from near-universal single-copy orthologs
Estimating transcript abundance
可以分为基于比对和不基于比对两种，其中RSEM和eXpress是基于比对的，另外两种是基于比对的。
RSEM
RNA-Seq by Expectation-Maximization
网址 https://deweylab.github.io/RSEM/README.html
eXpress
quantifying the abundances of a set of target sequences from sampled subsequences
网址 https://pachterlab.github.io/eXpress/overview.html
kallisto
快到飞起
丰度估计中样本特异性和读长偏好性低
quantifying abundances of transcripts from RNA-Seq data
网址 https://pachterlab.github.io/kallisto/
salmon
quantifying the expression of transcripts using RNA-seq data
网址 https://combine-lab.github.io/salmon/
也是很快
Read count
htseq-count
网址 http://htseq.readthedocs.io/en/release_0.9.1/
数read, 有它就够了
Difference expression
和之前的步骤对应，这里也可以分为基于read和基于组装以及不基于比对三类工具。
limma
Linear Models for Microarray Data
网址 http://bioconductor.org/packages/release/bioc/html/limma.html
用于分析芯片数据
DEseq
网址 http://bioconductor.org/packages/release/bioc/html/DESeq.html
DEseq2
效果在几个工具中相对好
网址 http://bioconductor.org/packages/release/bioc/html/DESeq2.html
DEGseq
Identify Differentially Expressed Genes from RNA-seq data
网址 http://www.bioconductor.org/packages/2.6/bioc/html/DEGseq.html
edgeR
Empirical Analysis of Digital Gene Expression Data in R
网址 http://www.bioconductor.org/packages/release/bioc/html/edgeR.html
Ballgown
准确度有时不是很好
facilitate flexible differential expression analysis of RNA-Seq data
organize, visualize, and analyze the expression measurements for your transcriptome assembly.
网址 https://github.com/alyssafrazee/ballgown
sleuth
用来配合kallisto使用
网址 https://pachterlab.github.io/sleuth/about
Data visualization
数据可视化的工具可以分为本地版本和在线版本
IGV
Integrative Genomics Viewer
网址 http://software.broadinstitute.org/software/igv/
本地展示分析结果的不二选择
jbrowse
公开展示数据或者给合作者分享时的不二选择，快且好看。
网址 http://jbrowse.org/code/JBrowse-1.10.2/docs/tutorial/
DEIVA
Interactive Visual Analysis of differential gene expression test results
网址 http://hypercubed.github.io/DEIVA/
差异表达的可视化在线工具
Heatmapper
expression-based heat maps
pairwise distance maps
correlation maps
网址 http://www.heatmapper.ca/
用来话各种热图的在线工具
START
visualize RNA-seq data starting with count data
网址 https://kcvi.shinyapps.io/START/
基于shinny的一套RNA-seq数据可视化工具
几个神奇的网站
biostars
网址 https://www.biostars.org
R book
网址 http://r4ds.had.co.nz/
python guide
网址 http://docs.python-guide.org/en/latest/
bioptyhon
网址 http://biopython.org/DIST/docs/tutorial/Tutorial.html
Rosalind
网址 http://rosalind.info/problems/list-view/
bioinformatics tools
网址 https://omictools.com/
网址 https://bioinformatics.ca/links_directory/
data visualistion catalogue
网址 http://datavizcatalogue.com/index.html
References
生信技能树2017年8月27日公号师妹 你要的都在这里了