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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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There is not detailed_serogroup_info in the output folder #79

Closed juanjo255 closed 2 weeks ago

juanjo255 commented 1 month ago

Hello!

I am trying to use SeroBA for serotyping a paired-end sequencing of a cultivated pneumococcus which has high coverage.

At the end, I only got a pred.tsv that explicitly said what was my serotype. However, I would like to get more information, for example, about the percentage of identity. In the documentation, it said that the program would also output a detailed_serogroup_info, nonetheless it is not there. What could be wrong?

I downloaded seroBA using conda. I had to downgrade KMC to 3.1.2 and apply this patch for pysam.

I hope you can help me,

Thank you,

Juan

Oliver-Lorenz-dev commented 2 weeks ago

Hi Juan!

We are now maintaining a new version of SeroBA which has an updated database and output file structure: https://github.com/sanger-bentley-group/seroba

Could you try running this version of SeroBA?

SeroBA will only output a detailed_serogroup_info file if the serotype cannot be resolved by kmer identity alone. It may be the case that the serotype in question can be resolved just using kmer identity.

SeroBA will print out the kmer identities for each serotype in the reference database in the terminal - they should look something like this:

/seroba/build/bin/kmc -k71  -ci4  -m2 -t1 16453_2#11_1.fastq.gz /lustre/scratch127/pam/teams/team284/ol6/update_seroba_db/monocle_test/seroba_nextflow/work/00/28956b4bb142da8b823b47999b2895/temp.kmcox9kmae_/16453_2#11 /lustre/scratch127/pam/teams/team284/ol6/update_seroba_db/monocle_test/seroba_nextflow/work/00/28956b4bb142da8b823b47999b2895/temp.kmcox9kmae_
/seroba/build/bin/kmc_tools simple /lustre/scratch127/pam/teams/team284/ol6/update_seroba_db/monocle_test/seroba_nextflow/work/00/28956b4bb142da8b823b47999b2895/temp.kmcox9kmae_/16453_2#11 /seroba/database/kmer_db/01/01 intersect /lustre/scratch127/pam/teams/team284/ol6/update_seroba_db/monocle_test/seroba_nextflow/work/00/28956b4bb142da8b823b47999b2895/temp.kmcox9kmae_/inter
0.15774599146383667
/seroba/build/bin/kmc_tools simple /lustre/scratch127/pam/teams/team284/ol6/update_seroba_db/monocle_test/seroba_nextflow/work/00/28956b4bb142da8b823b47999b2895/temp.kmcox9kmae_/16453_2#11 /seroba/database/kmer_db/02/02 intersect /lustre/scratch127/pam/teams/team284/ol6/update_seroba_db/monocle_test/seroba_nextflow/work/00/28956b4bb142da8b823b47999b2895/temp.kmcox9kmae_/inter
0.11302211302211303

Hope this helps.

Oli

juanjo255 commented 2 weeks ago

Awesome. I will try it!

I will re-open if anything comes up.

Thank you very much Oliver.