生物信息学分析的常用软件

生物信息学分析的常用软件。值得推荐！

1) Genome Browsers

• UCSD Genome Browser (@youtube@bilibili)
• IGV (@youtube@bilibili)

2) DNA-seq

(2.1) Mapping and QC

• Remove adaptor: cutadapt, Trimmomatic
• Mapping: Bowtie2, STAR
• QC: fastqc

(2.2) Mutation

• Mutation discovery: GATK, Varscan
• Mutation annotation: ANNOVAR

(2.3) Assembly

• denovo assembly software: Trinity

(2.4) CNV

• Whole Genome Seq: Control-FREEC
• Whole exome Seq: CONTRA, ExomeCNV

(2.5) SV (structural variation)

• structural variation: Breakdancer

3) RNA-seq

(3.1) RNA-seq

• Expression Matrix: featureCounts, HTseq
• Differential Expression: Deseq2, EdgeR
• Alternative Splicing: rMATS
• RNA Editing: RNAEditor, REDItools
• …

(3.2) Single Cell RNA-seq (scRNA-seq)

4) Interactome

(4.1) ChIP-seq

(4.2) CLIP-seq

• Pre-process: fastqc
• Mapping: bowtie, novoalign
• Peak calling: Piranha, PARalyzer, CIMS

(4.3) Motif analysis

sequence

1. MEME motif based sequence analysis tools http://meme-suite.org/
2. HOMER Software for motif discovery and next-gen sequencing analysis http://homer.ucsd.edu/homer/motif/

structure

1. RNApromo Computational prediction of RNA structural motifs involved in post transcriptional regulatory processes https://genie.weizmann.ac.il/pubs/rnamotifs08/
2. GraphProt modeling binding preferences of RNA-binding proteins http://www.bioinf.uni-freiburg.de/Software/GraphProt/

5) Epigenetic Data（表观遗传）

(5.1) ChIP-seq

• Bi-sulfate data:
  • Review: Katarzyna Wreczycka, et al. Strategies for analyzing bisulfite sequencing data. Journal of Biotechnology. 2017.
  • Mapping: Bismark, BSMAP
  • Differential Methylation Regions (DMRs) detection: methylkit, ComMet
  • Segmentation of the methylome, Classification of Fully Methylated Regions (FMRs), Unmethylated Regions (UMRs) and Low-Methylated Regions (LMRs): MethylSeekR
  • Annotation of DMRs: genomation, ChIPpeakAnno
  • Web-based service: WBSA
• IP data:
  • Overview to CHIP-Seq: https://github.com/crazyhottommy/ChIP-seq-analysis
  • peak calling: MACS2
  • Peak annotation: HOMER annotatePeak, ChIPseeker
  • Gene set enrichment analysis for ChIP-seq peaks: GREAT

(5.2) DNAase-seq

• review : Yongjing Liu, et al. Brief in Bioinformatics, 2019.
• peek calling: F-Seq
• peek annotation: ChIPpeakAnno
• Motif analysis: MEME-ChIP

(5.3) ATAC-seq

• pipeline recommended by Harward informatics
• peek calling: MACS2
• peak annotation: ChIPseeker
• Motif discovery: HOMER

6) Chromatin and Hi-C

More: Software for the ages