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See email and proposed solution from Thomas Berner on the galaxy-dev list http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-June/015103.html
He suggested adding a new `taxid_name.loc` file, e.g.
$ …
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I am getting the following results for a read:
readID seqID taxID score 2ndBestScore hitLength queryLength numMatches
cc722ee0-14cf-43a0-b53c-75ba10f250e4_Basecall_Alignment_template no rank 0 256 2…
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User requested feature; include the ability to optionally toggle colour coding based upon TaxID.
Should be achievable by accessing the TaxID from the gene elements in the JSON & updating the concep…
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Hi,
I'm trying to use this tool but it's unclear where the names and nodes files comes from in the documentation.
```
$ metaDMG config raw_data/alignment.sorted.bam \
--names raw_data/names-mdm…
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Hi,
I have been using Taxoniq successfully for some time but now many of the accessions I am looking for are not being found.
I use the following command line:
`t = taxoniq.Taxon(accession_id="PSS2…
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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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Hi
Firstly I have found the documentation and usage of mmseqs2 for taxonomic assignment to be extremely good and easy to follow!
However, just a quick point that some of the ncbi taxids given do…
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Hi,
Thank you very much for creating a good tool Ganon, I am using Ganon for taxonomic profiling but my target is not only bacteria and viruses, but also to identify species belonging to algae, fungi…
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I've run into this issue using PanGIA command line. Logs are attached:
```
[00:00:00] Starting PanGIA 1.0.0-RC6.1
[00:00:00] Arguments and dependencies checked:
[00:00:00] Input reads …
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The "--id_name_map" option currently requires that the user provide a version of the 'rankedlineage.dmp' file downloaded from NCBI. This works well for NCBI-supported taxIDs, but does not support cust…