Comments (2)
Hi Francisco,
Thanks a lot for the explanation, that sounds very reasonable.
And thanks for the pipeline again!
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Hi vrmarcelino,
Good question! Indeed, we cannot be sure that the microbes will grow in isolation, and the gapfilling is meant to ensure that the microbes can grow within the community. By default, the gapfilling is done with complete media (M8 in the config file/media_db.tsv, see figure 1d here), which assumes that the microbes should be able to grow in a community/environment where all nutrients are provided. In the metaGEM paper we gapfill on M8 and then simulate on M11 to observe exchanges associated with aromatic amino acids. Also note that the gapfill flag will use reaction confidence scores to prioritize the introduction of reactions/pathways with the most genetic evidence present in the contigs, i.e. not just adding random reactions until growth is achieved. Also, the log files of the carveme jobs will say how many metabolites/reactions are added from gapfilling, and from my experience it is usually none or in the low single digits.
Thanks for your interest in metaGEM and let me know if you have further questions!
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Related Issues (20)
- feature: add dead-end counter for assembly evaluation
- Installation error HOT 5
- feature: test & enable bioconda installation on macbook HOT 1
- improvement: use `wc` to count bp instead of summing contig header info for abundance HOT 1
- low number of species after binning for metaGEM model reconstruction HOT 2
- automate the response to y/n HOT 6
- [Question]: Install on mac M2? HOT 5
- CompositionVis & modelVis output HOT 7
- Job submission with qsub HOT 2
- [Bug]: 'BiGG_gene' is both an index level and a column label, which is ambiguous. HOT 4
- [Usage]: running workflow on workstation with local flag HOT 17
- Questions about media, gapfilling, and predicting interactions HOT 11
- Getting the following error while running the bash metaGEM.sh -t check
- Getting the following error while running the bash metaGEM.sh -t check HOT 8
- refined_bins output remains empty after successful binRefine step HOT 2
- [Question]: How to define and construct a custom culture medium component that can be recognized by CarveMe? HOT 2
- [Question]:Why, when I use CarveMe for gap-filling, does it show that my custom medium does not exist in the database? HOT 1
- [Question]: I meet some errors when I use CarveMe for gap-filling? HOT 3
- [Question]: How to use the GEM output of CarveMe to generate these two files? HOT 1
- [Bug]: Metawrap Installation failure HOT 5
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