Bacterial genome assembly workflow for paired end data (v1.0)

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

1. Assembly raw reads to a final contig fasta file
   • Shovill
2. Quality control of the assembly
   • Quast
   • Bandage to plot assembly graph
   • Refseqmasher to identify the closed reference genome
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 trimmed reads in fastq(.gz) format.

Outputs

1. Assembly:
   • Assembly with contig in fasta
   • Mapped read on assembly in bam format
   • Graph assembly in gfa format
2. Quality of Assembly:
   • Assembly report
   • Assembly Graph
   • Tabular result of closed reference genome
3. Aggregating outputs
   • JSON file with information about the outputs of Shovill, Quast, Bandage, Refseqmasher