longtianpy/bioinfoguide

Guidance to Bioinformatics in Vinatzerlab

Guidance to the bioinformatics tools used in Vinatzer Lab

This book introduces the bioinformatics tools and analyses in Vinatzer Lab. Originally by Dr. Alex Weisberg, I have made changes to some of the tools according to newer version and added introductions to new tools.

First thing First

while accessing the lab server using ssh, remember to add -Y for enabling the display variable of remote accessing. If not, the server will not be able to generate plots or launch GUI at your desktop/laptop.

Content

1. Downloading genome assemblies from NCBI GenBank
2. Assembling genomes with SPAdes
3. BIGSdb installation information
4. Core- and Pan-genome analyses using GET_HOMOLOGUES
5. Phylogenetic analysis with RAxML
6. LIN code assignment
7. To copy files to the server
8. List of software installed on the server
9. Phylogenetic analysis with RAxML
10. Search and replace inside a file using a table of search and replace terms