README.md

Helpful resources for microbial genomics

If you were not able to follow the video, here is the link to illumina Sequencing

[HOME]

General Bioinformatics resources

• Omictools

• Bioinformatics One-liners by Stephen Turner

• QC Fail: Explaining your errors

Short read processing

• FastQC

• Trimmomatic: Home Manual

• bwa

• bowtie

• samtools

• vcftools

• bcftools

• gatk

• picard

• SPANDx

• Snippy

Genome assembly

• Spades

• Velvet

• Mira

• A5

Genome alignment

• Mauve

• MUMmer

• Mugsy

Visualization of genomic data

• Artemis

• Artemis Comparison Tool

• IGV

Genome annotation

• Prokka

• Blastall

• LS-BSR

Phylogenetic tools and resources

• Visualization

  • Seaview

  • iTOL

  • Figtree

• Phylogenetic software

  • PAUP

  • RaxML

  • PhyML

  • BEAST

  • PHYLIP

  • APE

  • Microreact

  • Recombination detection

    • Gubbins

    • ClonalFrame

    • List of Phylogeny Programs

Databases

• ARDB

• PATRIC

Video Resources you should watch and follow

• FastQC

• NHGRI

• Broad Institute

• Cold Spring Harbor Lab

• NCBI

• Bioinformatics courses from MIT

• Youtube Channel of Rafael Irizarry covering various topics on NGS analysis and statistics involved in it.

101 Questions: a series of interviews with notable bioinformaticians

Bioinformatics is just like bench science and should be treated as such

Unix/Command line

• command-line bootcamp

• Code academy