zsutx2005 / bioinfo-pipelines

Sample bioinfo script collection.

Bioinfo-pipelines

There are three main parts of this repo:

• bioinfo_raining: Notes& summary of computational biology training course (for third-year undergrates)
• cpg_analysis: Pipeline notes on chloroplast genome analysis (with a focus on assembly for now )
• RNA_seq: RNA-sequencing based analysis notes (still in preparation)

Check each individual folder for details:D

And the folder bioinfo_raining includes notes on:

Lecture 1: Linux
Lecture 2: Python
Lecture 3: Biopython, SVG
Lecture 4: Regular expression in python, R
Lecture 5: Gomeme assembly(Velvet)
Lecture 6: Transcriptome assembly
Lecture 7: Intro to Genomic Annotation(no handson exercise)
Lecture 8: Construct phylogenic trees(Mega, JModelTest)
Lecture 9: Summary of previous lectures...
Lecture 10: SSR analysis(Krait)
Lecture 11: Gene family
Lecture 12: Align
Lecture 13: Call SNP
Lecture 14: Evaluate diversity
Lecture 15: Calculate PSMC
Lecture 16: Fastsimcol