Workflows
What is a Workflow?Filters
Query
Created At
Updated At
Tool
BUSCO5
MultiQC5
Stacks5
FastQC4
Bwa-mem23
QUAST3
Bandage2
BEDTools2
fastp2
Flye2
Minimap22
Racon2
SAMtools2
StringTie2
Biopython1
compute_sequence_length1
Cutadapt1
FASTX-Toolkit1
FGENESH1
GenomeScope 2.01
gfastats1
ggplot21
HISAT21
Medaka1
Merqury1
NanoPlot1
RepeatMasker1
RepeatModeler1
seqtk1
TransDecoder1
Trimmomatic1
YaHS1
More...
Workflow type
Galaxy26
Tag
Large-genome-assembly9
TSI-annotation7
TSI2
BUSCO1
genome_assembly1
HiFi1
hifiasm1
Merqury1
Meryl1
nanopore1
QC1
Quast1
More...
Space
Australian BioCommons26
Collection
BioCommons ‘Bring Your Own Data’ Expansion Project17
TSI annotation workflows7
HiFi genome assembly on Galaxy1
Operation annotations
Sequence clustering6
Sequencing quality control4
Sequence assembly2
Sequence assembly validation2
De-novo assembly1
Maturity
Stable1
26
Workflows visible to you, out of a total of 26
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 ...
Trim and filter reads; can run alone or as part of a combined workflow for large genome assembly.
- What it does: Trims and filters raw sequence reads according to specified settings.
- Inputs: Long reads (format fastq); Short reads R1 and R2 (format fastq)
- Outputs: Trimmed and filtered reads: fastp_filtered_long_reads.fastq.gz (But note: no trimming or filtering is on by default), fastp_filtered_R1.fastq.gz, fastp_filtered_R2.fastq.gz
- Reports: fastp report on long reads, html; fastp report ...
Kmer counting step, can run alone or as part of a combined workflow for large genome assembly.
- What it does: Estimates genome size and heterozygosity based on counts of kmers
- Inputs: One set of short reads: e.g. R1.fq.gz
- Outputs: GenomeScope graphs
- Tools used: Meryl, GenomeScope
- Input parameters: None required
- Workflow steps: The tool meryl counts kmers in the input reads (k=21), then converts this into a histogram. GenomeScope: runs a model on the histogram; reports estimates. k-mer ...
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 ...
Assembly polishing; can run alone or as part of a combined workflow for large genome assembly.
- What it does: Polishes (corrects) an assembly, using long reads (with the tools Racon and Medaka) and short reads (with the tool Racon). (Note: medaka is only for nanopore reads, not PacBio reads).
- Inputs: assembly to be polished: assembly.fasta; long reads - the same set used in the assembly (e.g. may be raw or filtered) fastq.gz format; short reads, R1 only, in fastq.gz format
- Outputs: ...