search

phac-nml / staramr

Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.
Apache License 2.0
111 stars 25 forks source link

The plasmidfinder.tsv shows that there is no plasmid present #178

Closed qianxin-kxy closed 1 year ago

qianxin-kxy commented 1 year ago

Hello, I used the following code to predict plasmids for hundreds of strains of Acinetobacter baumannii,

$ staramr search --plasmidfinder-database-type enterobacteriales -o out *.fasta

but the plasmidfinder.tsv only showed the following prompt Isolate ID Plasmid %Identity %Overlap HSP Length/Total Length Contig Start End Accession and did not display a single plasmid. I don't know what to do

apetkau commented 1 year ago

Hello @qianxin-kxy

  1. You may want to consider removing --plasmidfinder-database-type enterobacteriales to search for everything in the PlasmidFinder database.
  2. You may want to search using other tools as well (such as https://github.com/phac-nml/mob-suite)
  3. Are you certain your dataset contains plasmids? Are these draft assemblies from whole-genome sequence data?
qianxin-kxy commented 1 year ago

Thank you for your reply and suggestions, I have tried the first two methods, and the result of the first one also shows that there are none(The genome of the strain I am using is a FASTA file assembled using SPAdes after second-generation sequencing);

The second method, I also encountered new problems and was unable to run successfully. I have already provided feedback to the author and am waiting for their response;

As for the third condition, I download a strain of Acinetobacter containing two plasmids on NCBI(https://www.ncbi.nlm.nih.gov/assembly/GCA_024749765.1) and try it out，the results also shows nothing in the file of plasmidfinder.tsv, So I guess the software you developed may not be able to analyze the plasmid of Acinetobacter baumannii.

apetkau commented 1 year ago

Okay. Thank you for trying out the different possible solutions. It is possible that staramr is not able to identify plasmids in Acinetobacter. Note, that the sequences being searched for to identify plasmids were defined in https://journals.asm.org/doi/10.1128/AAC.02412-14 and so there may be more information there.

apetkau commented 1 year ago

I am closing this issue for now.