GEMSTONE Workflows
GEMSTONE_Isolates_Illumina_PE
This workflow processes paired-end Illumina reads from bacterial isolates. It performs QA and QC, flagging low quality and contaminated samples. Performs de novo assembly with the shovill pipeline. Finds AMR, virulence, and stress genes with AMRFinderPlus, identifies and types plasmid contigs with MOB-recon, types sequences with TS-MLST, annotates them with Bakta, and infers taxonomy with GAMBIT. Optionally, it estimates taxa abundances with Kraken2 and Bracken and does strain-level identification with StrainGE.
GEMSTONE_Plate_Swipes_Illumina_PE
This workflow processes paired-end Illumina reads from plate swipes/plate bacterial metagenomes. It could also be used for broader bacterial metagenomic analysis. It removes human reads, performs QA and QC, and metagenomic assembly. Furthermore, it estimates taxa abundances with Kraken2 and Bracken, does strain-level identification with StrainGE, bins MAGs, performs AMR genotyping, and identifies plasmid contigs.
Marco Teixeira
Colin Worby
