Workflows

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 => ...

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: ...

This notebook is about pre-processing the Auditory Brainstem Response (ABR) raw data files provided by Ingham et. al to create a data set for Deep Learning models.

The unprocessed ABR data files are available at Dryad.

Since the ABR raw data are available as zip-archives, these have to be unzipped and the extracted raw data files parsed so that the time ...

Workflow for quality assessment of paired reads and classification using NGTax 2.0 and functional annotation using picrust2. In addition files are exported to their respective subfolders for easier data management in a later stage. Steps:

• FastQC (read quality control)
• NGTax 2.0
• Picrust 2
• Export module for ngtax

This is an experimental KNIME workflow of using the BioExcel building blocks to implement the Protein MD Setup tutorial for molecular dynamics with GROMACS.

Note that this workflow won't import in KNIME without the experimental KNIME nodes for BioBB - contact Adam Hospital for details.