How to generate Genbank format out of paired end fastq data? I've unmapped cleaned paired end sequence data in fastq format of a bacterial genome. I want to get a sequence data in Genbank format in the end. What are the exact steps that I have to follow in galaxy webserver and if in some point necessary, also using linux based apps? I would appreciate a lot of details.
The steps needed to assemble a genome in Galaxy are layed out in the Assembly training material from the Galaxy Training network. The software for this should be available on the main galaxy servers (e.g., usegalaxy.eu). Since you have a prokaryote, I suggest you follow the "Unicycler Assembly" workflow, which is also available on usegalaxy.eu.