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