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Hi @nlapier2 and @dkoslicki,
This is Chunyu and I have two questions regarding Metaglin.
1. I'm wondering if the default database used by Metaglin includes the genomes of all organisms in NCBI …
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Sample along “discrete” disturbances/perturbation (oils spills, O2 excursions, hurricanes, etc..) Plankton, animal, benthic – depending on context). Viruses archaea, bacteria, protists….
Sample:
S…
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Because this pipeline is going to be used by multiple project that have a variety of different host organisms it is needed to create a database that contains all these hosts. In the first place to be …
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We will typically just need to get clade assignments (and summarize to counts of clade assignments) for samples that were collected within a particular date range. We should be able to specify those …
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Dear members,
I was trying to download the databses for Archaea, Bacteria and virus using the below code
centrifuge-download -o library -P 20 -m -a "Any" -d "archaea,bacteria,viral" refseq > seqid…
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Dear Ben,
Thanks for this great tool.
I have tried to use it recently to map small RNAs to virus genomes. I was expecting 21 nt long reads to map, indicating that host immune system responded t…
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Hi. I have encountered hundreds of unmapped accessions, for examples NZ_LS483329, when building database from virus, bacteria, archaea, fungi, protozoa and human reference genomes, with est, gb, gss a…
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hi,
I download the vOTU.fna (There are 5251 vOTUs in there.)data in the text and used the MGV pipeline(https://github.com/snayfach/MGV/tree/master/viral_detection_pipeline), like this
````
cond…
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Dear KVD-lab,
I appreciate your large effort to maintain and update PuMA.
I met some trouble with a Docker version of PuMA v1.2.1 . Processing PaVE's HPV41REF.1 occurs the following error:
``…
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kraken-build --standard --db $DBNAME
Only build Bacteria and Viruses, plasmids and human are not downloaded.
Not sure this is a bug or standard feature.
kraken-build --download-library plasmids --db …