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, TrimmomaticMapping: Bowtie2, STARQC: fastqc
(2.2) Mutation
Mutation discovery: GATK, VarscanMutation annotation: ANNOVAR
(2.3) Assembly
denovo assembly software: Trinity
(2.4) CNV
Whole Genome Seq: Control-FREECWhole exome Seq: CONTRA, ExomeCNV
(2.5) SV (structural variation)
structural variation: Breakdancer
3) RNA-seq
(3.1) RNA-seq
Expression Matrix: featureCounts, HTseqDifferential Expression: Deseq2, EdgeRAlternative Splicing: rMATSRNA Editing: RNAEditor, REDItools...
(3.2) Single Cell RNA-seq (scRNA-seq)
4) Interactome
(4.1) ChIP-seq
(4.2) CLIP-seq
Pre-process: fastqcMapping: bowtie, novoalignPeak 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, BSMAPDifferential Methylation Regions (DMRs) detection: methylkit, ComMetSegmentation of the methylome, Classification of Fully Methylated Regions (FMRs), Unmethylated Regions (UMRs) and Low-Methylated Regions (LMRs): MethylSeekRAnnotation of DMRs: genomation, ChIPpeakAnnoWeb-based service: WBSAIP data:
Overview to CHIP-Seq: https://github.com/crazyhottommy/ChIP-seq-analysispeak calling: MACS2Peak annotation: HOMER annotatePeak, ChIPseekerGene set enrichment analysis for ChIP-seq peaks: GREAT
(5.2) DNAase-seq
review : Yongjing Liu, et al. Brief in Bioinformatics, 2019.peek calling: F-Seqpeek annotation: ChIPpeakAnnoMotif analysis: MEME-ChIP
(5.3) ATAC-seq
pipeline recommended by Harward informaticspeek calling: MACS2peak annotation: ChIPseekerMotif discovery: HOMER
6) Chromatin and Hi-C
More: Software for the ages
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