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Kraken2 is an excellent tools to align microbial sequences.
While in each run, loading the database is a rather time-consuming process.
**I wonder if future developers could provide a way to lo…
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## Anti-microbial peptides
- [ ] LABiocin ([2019](https://doi.org/10.1016/j.ijantimicag.2019.07.012)). They require to make an account that takes some time to be validated and then you make a special…
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Dear @yinlabniu,
Thank you again for a very important tool to annotate CAZymes and identify CGCs in the microbial genomes of interest.
I am interested in examining how complete are the CGCs in my …
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Thanks for writing `taxor` and including useful databases!
What the community (or maybe just me) really wants is a database that covers more of the microbial kingdom, but with the benefit of GTDB f…
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@papanikos
I changed the strategy of running the programs of transeq and hmmsearch so each sample is run separately after length filtering step. Previously, samples were concatenated together before…
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This looks great! I think it might be good to add a references or refs folder. For genomics/microbial ecology project we often use references to map our data against or for classifying sequences. We f…
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Building a microbial nt database
Dear staff,
I am trying to build a microbial-nt database. According to the tutorial I run the following command:
_krakenuniq-download --db DB --taxa "archae…
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Hi! I have been using Kaiju for a while, and now I am interested in filtering fungal reads. For this, I used the Kaiju app in KBase and compared the results using two different databases: NCBI BLAST n…
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I am doing an experiment where we are testing 5 different ways to deplete host DNA on three types of low microbial biomass respiratory samples (sputum, nasal swabs, bronchoalveolar lavage) prior to de…
pslai updated
11 months ago
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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…