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)
- 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: ...
Germline-ShortV @ NCI-Gadi is an implementation of the BROAD Institute's best practice workflow for germline short variant discovery. This implementation is optimised for the National Compute Infrastucture's Gadi HPC, utilising scatter-gather parallelism to enable use of multiple nodes with high CPU or memory efficiency. This workflow requires sample BAM files, which can be generated using the Fastq-to-bam @ NCI-Gadi pipeline. Germline-ShortV can be applied ...
Fastq-to-BAM @ NCI-Gadi is a genome alignment workflow that takes raw FASTQ files, aligns them to a reference genome and outputs analysis ready BAM files. This workflow is designed for the National Computational Infrastructure's (NCI) Gadi supercompter, leveraging multiple nodes on NCI Gadi to run all stages of the workflow in parallel, either massively parallel using the scatter-gather approach or parallel by sample. It consists of a number of stages and follows the BROAD Institute's best practice ...