I plan to pre- process human stool shotgun metagenomes on Galaxy.eu and need a host-decontamination step before MetaPhlAn/HUMAnN. I couldn’t find KneadData in the tool panel,so I can’t filter human reads
Could you please let me know if it is possible from the admin team to Install KneadData or recommend the preferred Galaxy.eu tool for host read removal on human fecal shotgun metagenomics fastq files ?
My intended workflow within galaxy.eu is: Cutadapt → Host decontamination (KneadData or your recommendation ) → MetaPhlAn 3 → HUMAnN 3
Thanks a lot for your help and attention to my tool requests
I don’t think the Biobakery team has wrapped this for Galaxy yet. I don’t see it at their server or in the ToolShed, and I don’t see these workflow in the public Shared Data → Workflows area either.
Now, from what I understand, this protocol is more of a workflow than a distinct novel tool but I suppose it could be all combined on a Galaxy tool form. I checked the Biobakery forum and didn’t find any questions about this yet, or I missed the discussion.
For immediate processing, Run the Bowtie2 and other mappings directly in your own workflow. All of these tools are available and using a custom genome is possible. You don’t need to index it – Bowtie2 indexes are created at runtime. You only need the fasta in your history.
For later use, ask a question at the Biobakery forum about plans for this tool.
Big picture: Someone should put the wmgx protocol all together into an IWC workflow! https://iwc.galaxyproject.org/ I’m just mentioning it in case you or someone else reading is interested.
These tools are somewhat new, so maybe Galaxy workflows are already being planned. The Biobakery forum would be the place to ask about this as well. We would be interested in what happens, so if you want to crosslink the topic (add ours to their forum, then post back here with their link) that would be useful!
I’m also going to ask at the IUC matrix chat to see if anyone knows more but let’s keep this part of the conversation here.
