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We're testing this implementation of the LazyB, MuCHSALSA, on a metagenome with both Illumina and Pacbio reads. We're testing these hybrid assemblies for soil metagenomes.
The first sample is still …
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relevant to #309
I've been working on annotating catlases. In this use case, I built a "metapangenome" graph. I did a genome query (_R. gnavus_) in 605 gut microbiome metagenomes, and then combined…
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The rnaSpades mode is heavily focused on mRNA transcriptome assembly and is very aggressive at splicing assemblies into short transcripts. The —meta mode would be more suitable for our DNA/RNA assembl…
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### Description of bug
I tried to assemble metagenome reads via SPAdes (--meta), yet only the first k-mer can be assembled successfully without other manipulations. During the second k-mer assembly…
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### Description of feature
Decided I wanted to try and bin my data using Vamb, which isn't in the pipeline yet. Would be a useful feature to be able to supply a csv (or directory?) of bins and jump d…
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e.g. Input parameter is set to `--num_splits 12` but only 8 contigs are in the input
```
Error executing process > 'AUTOMETA:PRODIGAL (Annotating mock_metagenome)'
Caused by:
Process `AUTOME…
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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 Zhichao,
I got 55 MAGs from the 6 metagenome samples, but some typical genes for some MAGs were lost maybe during the binning or refinement process. So, is it okay that I use the assembled conti…
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For example,
Simply changing
**a**cerates viridiflora (raf.) eaton
https://api.gbif.org/v1/species/match?name=acerates%20viridiflora%20(raf.)%20eaton
to
**A**cerates viridiflora (raf.) eaton…
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"""
If time permits, I would suggest including in this publication, or a subsequent publication, the assessment of a more complex metagenome, which will challenge the assemblers more to have an even…