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These things don't need to go into the v1.0 release on conda but would be necessary to have in place before the paper is published for a well-dressed pipeline 😉
No due date•0/6 issues closedwe need to go on a final 2 week sprint to get somatem in order. don’t worry about the Omi integration, the key thing is making a functional and full featured pipeline that has been tested and deployed on a couple of systems. Really key features for me are 1. laptop/lightweight mode, 2. thorough documentation, 3. Clearly organized/labelled output directories for user perusal --- // Full featured = ? / refer to milstone v1 // Testing on which systems?
Overdue by 3 month(s)•Due by January 16, 2026•1/2 issues closedWe will make a fully functional and documented version of the Somatem pipeline to demo for lab to test out. Include connection to omi and running of taxonomic profiling through the webapp. Elaborate exact messages later.. Timeline for March in the discussion thread #80 : https://github.com/treangenlab/Somatem/discussions/80 Summary: General pipeline - Documentation: (**readme, tutorial, examples, uses cases**) - metro map of pipeline flowchart - **AI code review tool** : (cursor, claude code, gemini 3 pro/antigravity, else openai’s tool). - **prep a comparison of somatem to mmlongs2**. Minimal tax-profiling - prokaryotic: Emu, Lemur-magnet full - functional: viral, fungal: sylph Webapp / omi LLM - runs somatem through omi's last call - Needs a conda/docker for google cloud; needs v1 for that ? *so after Friday* Old Full message: we are going to go ahead and do a final demo for Wednesday October 22nd during lab meeting. for this demo I’d like to see: fully documented readme/repo, including citations to all papers included in the pipeline 2 to 3 tutorial/example datasets that successfully complete both the “assembly free” and “assembly” paths through the pipeline A final draft/fully functioning version of the core components (focusing on bacteria & metagenomic assembly) A first draft of a functioning viral metagenomics module (talk to Ryan if you need) An update on the status of the LLM (including feedback from Dongwei) (edited) 8:24 after next weeks meeting, we will start on the paper writing sprint. for that , we need to identify 3 use cases: comparison of read based to assembly based functional profiles of a gut microbiome community identification of motifs/SVs/HGT events in a microbiome (cheese dataset from rhea, or other) identification of a (viral) pathogen in a complex sample (BALF , wastewater, etc) **Key**: a complete and polished draft of the somatem paper absolutely needs to be ready 1 month from today, November 15th
Overdue by 5 day(s)•Due by April 30, 2026•5/9 issues closed