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Thanks for addressing the contamination issue (again)!
I am interested in cleaning up the NR database before using it for my application.
Would it be possible to also make available the list of…
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Hello,
Would it be possible to have the final confidence score reported in the output for each read? I'm exploring the use of this metric in calculating summary statistics for classified taxa (scor…
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I've been taking a deep dive into eukaryotic metagenomics and EukCC seems like a great tool to have in the repertoire. From the documentation, it seems that EukCC version 2 is still in development so …
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Hello, it's me again.
I wondered if the Microeukaryotic DB can be used with the MMSEQS2 taxonomy module. I am interested in using this database to assign taxonomy at the contig level rather than t…
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```
> kraken2-build --download-taxonomy --db ./RBCLDB
Downloading nucleotide est accession to taxon map...rsync: link_stat "/taxonomy/accession2taxid/nucl_est.accession2taxid.gz" (in pub) failed: No…
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When i run "hecatomb install", an snakemake error occurred. Do you have any ideas how to deal with it? Thanks a lot.
[2024:06:11 18:14:25] Copying system default config to hecatomb.out/hecatomb.con…
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Now that we're publishing FACTS to http://facts.contentmine.org/ (which is great!), it would be good to make some simple adjustments to the ami-species plugin to filter-out some false positives e.g. t…
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# Script
db="ncbi_nt/ncbi_nt"
kma -ipe A16_S5_3_F22_S139_R1_001.atria.fastq.gz A16_S5_3_F22_S139_R2_001.atria.fastq.gz -o A16_S5_3_F22_S139_out_kma -t_db $db -t 20 -1t1 -mem_mode -and -apm f
# …
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Hello every one,
I'm, trying to run the tool. However, after creating the DB via the mmseqs2 by my download NR.fasta that I had before, I run the homology search and I failed, and the feedback like …
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Current get children from taxids approach will not work if people are using their own taxonomies (by providing the KPCOFGS columns)
But, by the time metabin reaches the blacklisting step, it will a…