Workflows

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20 Workflows visible to you, out of a total of 20
Stable

Optional workflow to purge duplicates from the contig assembly.

Infrastructure_deployment_metadata: Galaxy Australia (Galaxy)

Type: Galaxy

Creator: Gareth Price

Submitter: Johan Gustafsson

Combined workflow for large genome assembly

The tutorial document for this workflow is here: https://doi.org/10.5281/zenodo.5655813

What it does: A workflow for genome assembly, containing subworkflows:

  • Data QC
  • Kmer counting
  • Trim and filter reads
  • Assembly with Flye
  • Assembly polishing
  • Assess genome quality

Inputs:

  • long reads and short reads in fastq format
  • reference genome for Quast

Outputs:

  • Data information - QC, kmers
  • Filtered, trimmed reads
  • Genome assembly, assembly graph, ...

Type: Galaxy

Creator: Anna Syme

Submitter: Anna Syme

DOI: 10.48546/workflowhub.workflow.230.1

Stable

Assembly, visualisation and quality control workflow for high fidelity reads built from circular consensus sequence (PacBio HiFi) data.

Infrastructure_deployment_metadata: Galaxy Australia (Galaxy)

Type: Galaxy

Creator: Gareth Price

Submitter: Johan Gustafsson

Stable

Conversion of files from BAM to FASTQ, including FASTQC & CCS.BAM file quality control (QC) steps.

Infrastructure_deployment_metadata: Galaxy Australia (Galaxy)

Type: Galaxy

Creator: Gareth Price

Submitter: Johan Gustafsson

Assess genome quality; can run alone or as part of a combined workflow for large genome assembly.

  • What it does: Assesses the quality of the genome assembly: generate some statistics and determine if expected genes are present; align contigs to a reference genome.
  • Inputs: polished assembly; reference_genome.fasta (e.g. of a closely-related species, if available).
  • Outputs: Busco table of genes found; Quast HTML report, and link to Icarus contigs browser, showing contigs aligned to a reference ...

Type: Galaxy

Creator: Anna Syme

Submitter: Anna Syme

DOI: 10.48546/workflowhub.workflow.229.1

Assembly polishing subworkflow: Racon polishing with long reads

Inputs: long reads and assembly contigs

Workflow steps:

  • minimap2 : long reads are mapped to assembly => overlaps.paf.
  • overaps, long reads, assembly => Racon => polished assembly 1
  • using polished assembly 1 as input; repeat minimap2 + racon => polished assembly 2
  • using polished assembly 2 as input, repeat minimap2 + racon => polished assembly 3
  • using polished assembly 3 as input, repeat minimap2 + racon => ...

Type: Galaxy

Creator: Anna Syme

Submitter: Anna Syme

DOI: 10.48546/workflowhub.workflow.227.1

Assembly with Flye; can run alone or as part of a combined workflow for large genome assembly.

  • What it does: Assembles long reads with the tool Flye
  • Inputs: long reads (may be raw, or filtered, and/or corrected); fastq.gz format
  • Outputs: Flye assembly fasta; Fasta stats on assembly.fasta; Assembly graph image from Bandage; Bar chart of contig sizes; Quast reports of genome assembly
  • Tools used: Flye, Fasta statistics, Bandage, Bar chart, Quast
  • Input parameters: None required, but recommend ...

Type: Galaxy

Creator: Anna Syme

Submitter: Anna Syme

DOI: 10.48546/workflowhub.workflow.225.1

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