/bioinformatic-pipelines

Include common methods in bioinformatics, including genome assembly (with and without reference genomes), and RNAseq processing.

Primary LanguageShellMIT LicenseMIT

Bioinformatic Fundamentals

Note: The original version is provided by Prof. Waldeyr Mendes Cordeiro da Silva, see on Github.

This tutorial contain four main parts available on manual directory (there is not also finished, thus take care):

  1. 01_environment_preparation: contains all scripts to prepare a local or docker machine for bioinformatic analysis;

  2. 02_de_novo_assembly: genome assembly without reference sequence;

  3. 03_with_reference_assembly: genome assembly with reference sequence;

  4. 04_rna_seq: explore RNAseq results.

If you're interested in trying this out, just clone the repository and execute the command pandoc *.md > markdown_book.html in the root directory of the repo (details for multi.md files repository preparation and compilation). Additional parameter would be supplied to produce a user friendly document:

pandoc -V geometry:margin=0.85in --highlight-style=breezedark *.md > markdown_book.html