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Bacterial gene prediction doesn't usually rely heavily on external evidence to generate gene models. JGI uses GenePrimp as a post-processor, whereas NCBI PGAP searches every single ORF
in the geno…
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Hi Dear author,
I recently found that in the result after predicting model 1 (read level result), there are some duplicate reads ID in the result as below:
```
20230917_11775_control_read_level…
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Hi!
I am trying to use Platon 1.6 installed with BioConda to identify plasmid contigs. By running the following command:
platon contigs.fasta --db ~/Databases/db --output platon_accu --mode accura…
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Now that there is a critical mass of minor improvements to be made, I am creating a master issue to organize all of the changes which will go into a new minor release. I am describing this as a minor …
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This is a proposal to improve feature profiling for the identification of tRNAs from tRNA-seq libraries and to benchmark the profiling algorithm with high-scoring tRNA gene predictions from a database…
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Hi,
I have a set of already called genes (not from prodigal) that I would like to use as input to inStrain. Is there any easy way to do this? Based on a previous issue (#56 specifically), it appear…
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Hi, I am trying to build my own Sourmash LCA database based on NCBI, SILVA, or Greengenes databases for taxonomic classification for my k-mer hash dataset (e.g. 7-mer) computed from 16S rRNA gene sequ…
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Thanks for this usefull tool, I'm going to use it to annotate my sequence.
However, I'm puzzled about the params `[-t {contig,protein}]`, it seems that in `contig` mode, input will treated as nucle…
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I recently came across this publication at github https://github.com/gavinmdouglas/q2-picrust2/issues/9 and it resonated with some queries I've had in mind.
I'd truly appreciate it if you could spa…
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I applied your script on my data. As you can see in the metadata I have a column called traitment with ( CTRL , TR1 ,TR2 and TR4)
ko_abundance_file