Quality and Contamination control workflow for paired end data (v1.0)

This workflow uses paired-end illumina fastq(.gz) files and executes the following steps:

1. Quality control and trimming
   • fastp QC control and trimming
2. Taxonomic assignation on trimmed data
   • Kraken2 assignation
   • Bracken to re-estimate abundance to the species level
   • Recentrifuge to make a krona chart
3. Aggregating outputs into a single JSON file
   • ToolDistillator to extract and aggregate information from different tool outputs to JSON parsable files

Inputs

1. Paired-end illumina raw reads in fastq(.gz) format.

Outputs

1. Quality control:
   • quality report
   • trimmed raw reads
2. Taxonomic assignation:
   • Tabular report of identified species
   • Tabular file with assigned read to a taxonomic level
   • Krona chart to illustrate species diversity of the sample
3. Aggregating outputs:
   • JSON file with information about the outputs of fastp, Kraken2, Bracken, Recentrifuge