• 微信公众号:美女很有趣。 工作之余,放松一下,关注即送10G+美女照片!

生物信息学分析的常用软件

互联网 diligentman 2周前 (02-18) 13次浏览

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)

生物信息学分析的常用软件

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

生物信息学分析的常用软件

 

编辑于 3 小时前


程序员灯塔
转载请注明原文链接:生物信息学分析的常用软件
喜欢 (0)