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