Full Pipeline Workflow¶
The Full Pipeline processes raw sequencing reads through trimming, assembly, annotation, and reporting.
Stages¶
1. Trimming¶
| Platform | Tool | Description |
|---|---|---|
| Illumina | Trim Galore | Quality and adapter trimming (wraps Cutadapt) |
| Nanopore | Porechop | Adapter removal for Oxford Nanopore reads |
2. Assembly¶
| Platform | Tool | Description |
|---|---|---|
| Illumina | SPAdes | De Bruijn graph assembler with careful mode |
| Nanopore | Canu | Overlap-layout-consensus assembler for long reads |
| Nanopore | Flye | Fast long-read assembler using repeat graphs |
| Nanopore | Unicycler | Hybrid assembler (can use both short and long reads) |
3. Annotation¶
All annotation tools from the Annotation Workflow are available.
4. Report¶
KEGG-decoder generates metabolic pathway visualizations from Prokka output.
Input Requirements¶
Illumina¶
- FASTQ files (
.fastqor.fastq.gz) - Single-end: one file per sample
- Paired-end: two files per sample (R1 and R2), must be uploaded together
Nanopore¶
- FASTQ files from MinION, GridION, or PromethION
- Basecalled reads (not raw FAST5)
PacBio¶
- FASTQ or BAM files from Sequel/Sequel II
Parameters¶
| Parameter | Required | Description |
|---|---|---|
| Genome Size | For Nanopore | Estimated genome size (e.g., 5m for 5 Mbp) used by Canu |
| Genus | Yes | Organism genus |
| Species | Yes | Organism species |
| Sample Name | Yes | Name for the analysis run |