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Ephie Geza, 02/06/2024 09:25 AM

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# Wiki
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## Data





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    Ephie Geza
    





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ARGannot





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## MLST





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To type certain sample pair, we first downloaded the MLST scheme for **Pseudomonas aeruginosa** and renaming files by





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``` shell





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img="/cbio/users/katie/singularity_containers/6c884bc3ab5c-2017-12-15-c6ae6fedbccd.img"





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singularity exec ${img} getmlst.py --species "Pseudomonas aeruginosa"





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mv Pseudomonas_aeruginosa.fasta Pseudomonas.fasta





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mv profiles_csv Pseudomonas_profiles_csv





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mv alleles_fasta Pseudomonas_alleles_fasta





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```





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This was also done for **Klebsiella pneumoniae**, **Enterobacter cloacae**, **Escherichia coli#1**, **Escherichia coli#2**. It is important to note that **Serratia does not have MLST profile at February 2024**.





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We now run MLST for each species using





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``` shell





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nextflow run /cbio/projects/033/uct-srst2/main.nf \





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        --reads '/cbio/projects/033/analysis/2024-01-11-fastq_QC/bbduk/Pseudomonas/*_{1,2}.fq'  \





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        -profile ilifu \





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        --mlst_definitions /cbio/projects/033/analysis/02_MLST/profiles/Pseudomonas_profiles_csv \





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        --mlst_db /cbio/projects/033/analysis/02_MLST/profiles/Pseudomonas.fasta \





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        --mlst_delimiter "_" --outdir /cbio/projects/033/analysis/02_MLST \





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        -resume -dsl1





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```





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### MLST results





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Most categorized alleles of the select group couldn't match with sufficient depthin the sequences of our short reads. Some fastq pairs had some **mismatches** represented by the number and an "*"





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## Reasons why MLST may fail





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 - No Match Found i.e sequence data of the specified loci doesn't have a match in the MLST database (variations, mutations, or target genes not present in MLST DB)





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 - Low-Quality Sequences or ambiguous base calls in the sequenced loci may cause MLST assignment to fail





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 - Incomplete Sequencing - the seq coverage sholud be sufficient and cover all required loci





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 - Database Mismatch - the DB used for typing should be appropriate for the organism or strain





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 - Novel Sequence Type - if isolate carries a novel or uncharacterized sequence type not present in the MLST database, most common when studying less common or newly emerging strains.





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## Antimicrobial Gene Detection





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Mapping reds of each reference seq in fasta format throough *--gene_db* to report all genes covered beyond 80% (default is 90%)