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**Submitting author:** @nselem (Nelly Selem)
**Repository:** https://github.com/carpentries-lab/metagenomics-workshop
**Branch with paper.md** (empty if default branch):
**Version:** v1.0.0
**Edi…
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**Submitting author:** @jinfinance (Rong Jin)
**Repository:** https://github.com/ncezid-biome/HMAS-QC-Pipeline2
**Branch with paper.md** (empty if default branch): main
**Version:** v1.2.0
**Editor:**…
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I generated a warning message while running ARGs OAP stage_one on the server. The metagenomic data is sourced from NCBI and has gone through the kneaddata process. However, when I used my own sequenci…
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Hi!
I'm working with a shotgun metagenomics data, and we aim to analyze the functional profile.
we have 224 samples in total, with 356 different pathways.
below are the codes that I used
metage…
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## Short description of the problem
I end up with different results per sample when I run co-assembly on all my samples at once vs going through the anvio pipeline for subsets of my files.
## an…
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We've had reasonably good results with [IVA], but it has a few problems:
1. Some samples are very slow, even taking multiple days. Random primers seem to be slow.
2. We find contigs with a lot of …
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Hi Kun_peng team,
Is it possible to provide some pre-built database out there just as original kraken2 did? E.g., one for GTDB v214 for species level purposes and also one for all NCBI/RefSeq genom…
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Hi all,
thanks for the awesome tool.
I am new to metagenomics and unsure if this is a squeezemeta-specific issue or common (Sorry if this is a repeat question too).
I get a low species-level …
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First thanks a lot for your detailed description of how to build the nt database using centrifuge (more detailed than at centrifuge's docs).
However, I cannot succeed with the last step. I got nt.f…
koppk updated
4 months ago
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In branch `PR10-type-slot-required-migration`
- https://github.com/microbiomedata/berkeley-schema-fy24/pull/66
partial project.Makefile:
```make
local/mongo_as_unvalidated_nmdc_database.yaml…