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We need to determine the best way to identify a reference species based on the assembled sequences (`contigs.fa`). Current ideas have touched upon MASH, but also Jspecies, etc. Still no solution.
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Please consider adding to your host list Citrus maxima (pomelo) with the accesion number MKYQ00000000.1 and Azadirachta indica (mahogany) with the accesion number AMWY00000000.2.
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I have been trying to assemble a bacteria genome of 2.5mb with a high coverage 1800X PacBio data, but had no luck. I tried a few parameter suggested, None of them gave me ideal continous contigs.
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Hi, I am trying to run Breseq/0.31.0 on some evolved bacterial isolate Illumina data (resulting from experimental evolution) which I am trying to compare to its ancestral strain via consensus mode, an…
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Hi all,
I have 1d and 1d2 nanopore reads for a GC-rich microbial genome. Does anyone have experience combining these data? Is it worth it?
Thanks for any thoughts!
**Edited to add:**
1d re…
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I have been using a script to parse GenBank files to find taxonomic information corresponding to bacterial genomes. After several tries, my script has failed with the following error:
...
`Bacteri…
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Getting an error when trying to run `jsa.np.rtResistGenes`.
Example script that is being used to run is
```
jsa.np.npreader --folder=$1 --output=- | \
…
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The PHYLIP format for distance matrices only allows identifiers of up to 9 (or 10?) characters. Unfortunately this means that sometimes names are cutoff, making them indistinguishable. A `--name-lengt…
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Hi,
I'm new to nullarbor but the pipeline seems great.
I started a test (3 bacterial genomes in Illumina PE) to see if the installation was good (for the installation I used linuxbrew and folloed …
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Following the approach of [Shinzato et al. (2014)](dx.doi.org/10.1371/journal.pone.0085182) (see Table S3), I've blasted the Pdam scaffolds against both the *Acropora digitifera* and *Symbiodinium min…