TheiaProk

The TheiaProk workflows are for assembly and characterization of prokaryotic genomes, principally bacteria. All input reads go through steps in the core workflow for read trimming and assembly, quality assessment, species identification and resistance gene identification. Sub-workflows further characterize some genomes, with activation of these processes dependent on the taxa identified.

Currently, there is one TheiaProk workflow. This is for reads generated with Illumina paired-end sequencing. Further workflows taking in alternative sequence data types may be developed.

TheiaProk_Illumina_PE

TheiaProk_Illumina_PE workflow

Inputs: TheiaProk_Illumina_PE takes in Illumina paired-end reads with an average genome depth of coverage of [x] X. By default, the workflow anticipates 2 x 150bp reads. For other read lengths, modification of the default trimming parameters is recommended. For more details about TheiaProk_Illumina_PE input files, see the tables of required inputs and optional inputs.

Core-workflow

Quality trimming and adapter removal: Trimmomatic, BBDuk

De Novo assembly: Shovill

QC: FASTQ-SCAN (reads before and after trimming); Quast (assemblies)

Core sample characterization: AMRFinderplus for ARG detection; Gambit for taxa identification; MLST (available MLST schemes)

NCBI’s AMRFinderplus identifies gene sequences associated with acquired antibiotic resistance. For a list of curated organisms that can be found here, acquired genes that are almost universal in a taxa (“intrinsic reistsance” genes) are filtered out, and/or mutational resistance and/or genes for virulence and stress response can be identified.

Implementation of NCBI’s AMRFinderplus in TheiaProk queries sequences against genes in NCBI’s curated database, > reporting sequences with > 90% identity (or a or curated threshold if it exists for the taxa) and a minimum coverage of 50 %.

Taxa-specific subworkflows

  • Salmonella spp: SeqSero2, SISTR, GenoTyphi

  • Escherichia spp: SeroTypeFinder, ECTyper

  • Klebsiella spp: Kleborate

  • Listeria spp: LisSero, Legsta

  • Mycobacterium tuberculosis: TB-profiler

Outputs: The workflow produces trimmed reads, assembly files, QC metrics and genome characteristics, depending on taxa analyzed. For more details about TheiaProk output files, please see the table of `outputs <>`_