Pipeline Overview

Pipeline Summary:

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QC

1. PhiX174 read removal and adapter removal using BBDuK

2. Filtering, trimming, and base correction using fastp that includes:

   • quality trimming with a window size of 20 and quality of 30
   • quality pruning at 3' and 5' ends
   • removal of short reads
   • forced polyG tail trimming

3. Contamination check of trimmed reads using Kraken2 and Kraken2.

Analysis of Trimmed Reads

4. QC Metrics Generated (all data generated for paired and unpaired reads generated post-trimming):
   • Number of total reads/bases
   • Percent of reads/bases remaining (from raw sequences)
   • Number of Q20/Q30 bases
   • Percent Q20/Q30 bases

Analysis using Trimmed Reads

This step is only run with -entry CDC_PHOENIX

5. Gene detection and allele calling for antibiotic resistance (AR) srst2 in gene mode. We have curated an AR gene database that is a combination of three AR gene databases with redundancies removed and gene names standardized.

• The curated AR gene database includes complete genes from these AR gene databases:
  • AMRFinderPlus
  • ARG-ANNOT
  • ResFinder

Assembly

6. Assembly of trimmed reads using SPAdes
7. Filter reads to remove any scaffolds less than 500bp in length.

QC of Assembled Scaffolds >= 500bps

8. Assess assembly quality using QUAST and custom scripts
9. QC Metrics Generated:
   • Raw coverage (total raw bases / assembly length)
   • Trimmed coverage (total trimmed bases / assembly length)
   • Assembly ratio (assembly size / median genome size of species)

Analysis of Assembled Scaffolds >= 500bps

10. Assess genome assembly for completeness using BUSCO. This step is only run with -entry CDC_PHOENIX
11. The mast distance is calculated from a pre-calculated sketch created with Mash and the top 20 best matches are passed into FastANI for increased speed in species ID.
12. Calculate the average nucleotide identity (between genomes) using FastANI to determine species.
13. Type multiple loci to characterize isolates of microbial species using MLST
14. AR genes and hypervirulence genes are detected using GAMMA. We have curated an AR gene database that is a combination of three AR gene databases with redundancies removed and gene names standardized. Plasmid markers are detected with GAMMA-S.

• The curated database includes genes from these AR gene databases:

  • AMRFinderPlus
  • ARG-ANNOT
  • ResFinder

• Additional databases are used:

  • Database of hypervirulence genes from Russo et al.
  • PlasmidFinder

15. AMRFinderPlus is run and the point mutations are reported in the Phoenix_Output_Report.tsv
16. In addition to running Kraken2 on the trimmed reads, KRAKEN2 is run on the weighted assembled scaffolds using the same database. This additional step allows us to check if any contamination made it into the assembly and this taxa call will be used if FastANI fails.

This step is only run with -entry CDC_PHOENIX