生物資訊學分析的常用軟體，值得推薦！
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
- MEME motif based sequence analysis tools http://meme-suite.org/
- HOMER Software for motif discovery and next-gen sequencing analysis http://homer.ucsd.edu/homer/motif/
structure
- RNApromo Computational prediction of RNA structural motifs involved in post transcriptional regulatory processes https://genie.weizmann.ac.il/pubs/rnamotifs08/
- GraphProt modeling binding preferences of RNA-binding proteins http://www.bioinf.uni-freiburg.de/Software/GraphProt/
5) Epigenetic Data（表觀遺傳）
(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
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