Skip to content
master
Switch branches/tags
Go to file
Code
This branch is even with Arkadiy-Garber:master.

Latest commit

 

Git stats

Files

Permalink
Failed to load latest commit information.
Type
Name
Latest commit message
Commit time
 
 
 
 
 
 
 
 

README.md

Binder for BVCN AntiSMASH lesson

Initially forked from here. Thank you to the awesome binder team!

Binder

Part of the Bioinformatics Virtual Coordination Network :)

Walkthrough

Put bioinf_tools into PATH

export PATH="${PATH}:/home/jovyan/MagicCave:/home/jovyan/bioinf_tools"

Download antismash databases

download-antismash-databases

Print the antismash help menu

antismash -h

Run the simplest version of the command

antismash Sodalis_praecaptivus-fixed.gbk

Run the simplest version of the command with an assembly

antismash --genefinding-tool prodigal Sodalis_praecaptivus-fixed.fasta

Convert GenBank output file to FASTA format

bit-genbank-to-fasta -i NZ_CP006569.1.region001.gbk -o NZ_CP006569.1.region001.fasta
bit-genbank-to-AA-seqs -i NZ_CP006569.1.region001.gbk -f NZ_CP006569.1.region001.faa

Print full help menu

antismash --help-showall

Run antismash with additional analyses

antismash --genefinding-tool prodigal --fullhmmer --pfam2go --asf --cb-knownclusters --clusterhmmer --cf-create-clusters Sodalis_praecaptivus-fixed.fasta

About

No description, website, or topics provided.

Resources

Releases

No releases published

Packages

No packages published