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sanger-pathogens / seroba

k-mer based Pipeline to identify the Serotype from Illumina NGS reads
https://sanger-pathogens.github.io/seroba/
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serotyping from assemblies as input #65

Open abrozzi opened 2 years ago

abrozzi commented 2 years ago

Dear Friends,

I don't have reads, but assemblies (one or mere contigs) of S. pneumoniae. How can I assign the serotype? seroBa doesn't look like to support fasta input right?

Bests, Alex

hujingchu commented 2 years ago

Hi Alex, Did you find any solutions to serotyping directly from assemblies directly?

abrozzi commented 2 years ago

Dear Hu, thank you for reaching out! No, I didn't. I found a workaround downloading from NCBI Bioproject serotyping information (when present). It would be nice to have for Pneumonia a tool like Kaptive https://github.com/katholt/Kaptive/wiki/Interpreting-the-results

I will keep you updated if I am aware of a serotyping directly from assemblies directly.

With Regards

Alessandro Brozzi, GSK Vaccines (Italy)

hujingchu commented 2 years ago

Dear Alex, Thanks you for the information. I tried by mapping reference sequence of different serotype directly to the assembly genomic sequence via minimap2, then choosing the the best hit (mapping quality, length and diversity rate), after checking couples of assemblies from refseq, it seems works Best, JC