Genomic characterization of pathogens is an increasing priority for public health laboratories globally. The workflows in the TheiaMeta Genomic Characterization Series make the analysis of pathogens from metagenomic samples easy by raw next-generation sequencing (NGS) data as input to retrieve sequences to the most up-to-date international standards.

The TheiaMeta workflow series consists of the following workflows, each for a different input data type:

Illumina paired-end data (TheiaMeta_Illumina_PE workflow)

Inputs

The TheiaMeta_Illumina_PE workflow processes Illumina paired-end (PE) reads generated for metagenomic characterization (typically by shotgun). By default, this workflow will assume that input reads were generated using a 300-cycle sequencing kit (i.e. 2 x 150 bp reads). Modifications to the optional parameter for trim_minlen may be required to accommodate shorter read data, such as 2 x 75bp reads generated using a 150-cycle sequencing kit.

Workflows available

Overview

Inputs

Required User Inputs

Optional User Inputs

Outputs

Terra Outputs

References