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## The need
A better `anvi-script-gen-short-reads` to generate more realistic short-reads from longer sequence.
I want to turn long-read metagenomes into short-reads metagenomes.
## The soluti…
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The NCBI taxonomy database is a database, not an ontology. As such that automatic translation includes various things that are not ideal from an ontology modeling perspective
If we were to make the…
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I have recently used VIBRANT with a metagenomics dataset with very good results, and I wonder if VIBRANT can also be run skipping the recovery step. I have few hundreds viruses that I recovered from s…
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Need to download and start coassembly of data set suggested by Meren:
Here are the metagenomes:
https://www.ncbi.nlm.nih.gov/sra/?term=SRP093449
This archive contains FASTA files for every bi…
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- Graph construction was implemented using `rustworkx` in #234, I want to mention that the `rustworkx` python interface is remarkably optimized. Using Python, we can build all graph-downstream analyse…
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Hi Gherman, hope everything is OK.
I have updated metaWRAP, and am trying to use it to analise 5 metagenomes. I already used with success all commands till assembly, and now I was trying to use KRA…
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Hi
I used contigs mode o bin the metagenomes (long-reads).
Then I am trying to run the separate_reads.py and I am getting the following error:
```
Traceback (most recent call last):
File "sepa…
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I put together a notebook for tracking workflow using sourmash here:
https://github.com/bioinfonm/bat_metagenomics_2016/blob/master/python_code/sourmash_CAVE_bat_metagenomes.ipynb
Change log:
pylab.s…
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I have obtained bins with a gene-based binning, these genes are generally short (
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This issue can serve as a placeholder for use cases for sourmash/MinHash more generally.
Stuff we already have implemented:
* basic MinHash comparisons etc
* metagenome taxonomy breakdown
* st…