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Bacterial Genome Assembly using Shovill

Assembly of bacterial paired-end short read data with generation of quality metrics and reports

  • Author(s):
  • abromics-consortium
  • ABRomics
  • Pierre Marin
  • Clea Siguret
  • Release: 1.1.3
  • License: GPL-3.0-or-later
  • UniqueID: bfe7f341-07ef-4bfe-9b50-2bc7628d6c55

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