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Sample bioinfo script collection.
Python Shell Perl OpenEdge ABL q Smarty R
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bioinfo_training
cpg_analysis
population genetics
rna_seq
.DS_Store
README.md

README.md

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
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