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srst2 AMR and VFDB results transferred

In addition to MLST analsysis srst2 turned out to be a very good tool for VF and AMR detection. Srst2 was implemented on Ilifu (nextflow pipeline) and the result were transferred to athena
Added by Katie Lennard almost 6 years ago

NB: there were some differences in results between Tychus and srst2 which seems to be due to different bowtie2 parameter settings, resulting in differences in alignments. Tychus uses default parameters while srst2 has been optimized for sensitive local alignments with the --very-sensitive-local and -a flags I therefore think we should use srst2 which has been carefully optimized for MLST and gene detection. Furthermore, there appears to be several redundant/duplicate entries in the ResFinder DB, whereas the ARGannot DB that is supplied with srst2 has been curated. Attached an example of differences in alignment, using the same DB and reads (but different bowtie2 settings between the two pipelines).

VF and AMR detection were run against VFDB and ARGannot as described in the srst2 github repo with default settings https://github.com/katholt/srst2#all-usage-options

  • VF results and relevant DB file and README copied to medmicro/Clinton/Ps_aerug/Katie_results/Ps_aerug_srst2_VFDB/
  • MLST and AMR results + relevant DB files and README copied to medmicro/Clinton/Ps_aerug/Katie_results/Ps_aerug_srst2_MLST_argAnnot/
igv_snapshot_catB7.png (32.4 KB) igv_snapshot_catB7.png Katie Lennard, 05/14/2019 12:18 PM
srst2_resfinder_cat7B_igv_snapshot.png (36.2 KB) srst2_resfinder_cat7B_igv_snapshot.png Katie Lennard, 05/14/2019 12:18 PM

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