Workflows

Data QC step, can run alone or as part of a combined workflow for large genome assembly.

• What it does: Reports statistics from sequencing reads.
• Inputs: long reads (fastq.gz format), short reads (R1 and R2) (fastq.gz format).
• Outputs: For long reads: a nanoplot report (the HTML report summarizes all the information). For short reads: a MultiQC report.
• Tools used: Nanoplot, FastQC, MultiQC.
• Input parameters: None required.
• Workflow steps: Long reads are analysed by Nanoplot; Short reads ...

Assembly polishing subworkflow: Racon polishing with short reads

Inputs: short reads and assembly (usually pre-polished with other tools first, e.g. Racon + long reads; Medaka)

Workflow steps:

• minimap2: short reads (R1 only) are mapped to the assembly => overlaps.paf. Minimap2 setting is for short reads.
• overlaps + short reads + assembly => Racon => polished assembly 1
• using polished assembly 1 as input; repeat minimap2 + racon => polished assembly 2
• Racon short-read polished ...

This is a Galaxy workflow that uses to convert the16S BIOM file to table and figures. It is part of the metaDEGalaxy workflow MetaDEGalaxy: Galaxy workflow for differential abundance analysis of 16s metagenomic data.