Hi everybody, I need some help. I am working on Galaxy in a new genome. I used the SPADEs tool for ensembling my sequences and it generated about 130.000 sequences.
My question is if there is some tool in Galaxy that decreases the number of gaps and gets contigs larger as chromosomes. I appreciate any help you can provide.
Welcome, @Bioinformatica_INBIO
It sounds like you are at the first step in contig building. The next steps usually require specific types of long reads, so the exact tool to use can vary depending on which you have or plan to generate.
This tutorial is a good place to start. https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/tutorial.html#assembly-polishing
The VGP tutorials cover slightly different data/tools. https://training.galaxyproject.org/training-material/topics/assembly/tutorials/vgp_genome_assembly/tutorial.html#scaffolding
You can explore the other Assembly tutorials at that site in the same category, then Genome Annotation tutorials will cover what you’ll probably want to do next.
All of these tutorials have publication link outs to provide some more context. If you find some other tool mentioned in those, check the tool panel at a public Galaxy server to see if someone has wrapped it already or if a similar tool is available. Other tools can be wrapped as justified/needed.
Now, not all tools are included in a tutorial but you’ll usually find examples and more link outs down in the help section on each form: related publications, author resources.
Hope that helps!
Hi Jennifer, thanks so much for writing. I will check what you sent me. I’m afraid that I don´t have long reads and maybe it would be a problem to reach a complete chromosome.
Thanks again. I´ll probably ask more questions soon.
My regards