Sequana LORA
sequana_lora is a Sequana pipeline for de novo assembly of long-read sequencing data (ONT, PacBio HiFi). It combines read quality control, assembly, polishing, and coverage analysis into a single Snakemake workflow, producing rich interactive HTML reports at every step.
This page hosts example HTML outputs generated by sequana_lora on real datasets so you can explore the reports without running the pipeline yourself.
Overview
The pipeline covers the following stages:
- Quality control — long reads QC
- Assembly — Flye / Hifiasm / Canu / Pecat / Necat / Unicycler, contig stats via QUAST
- Completeness assessment — checkM, BUSCO
- Coverage analysis — sequana_coverage per-contig HTML reports
- BLAST annotation — top-hit taxonomic assignment of contigs
- Graph visualisation — Bandage assembly graph
- Summary — consolidated pipeline HTML report
Demo dataset
The reports below were produced from PacBio HiFi reads of Streptococcus (original data: PRJNA94176). The HiFi dataset used here is archived on Zenodo (10.5281/zenodo.17207091) and consists of 5 samples: one full sample and four sub-sampled versions created for demonstration purposes, allowing you to observe how assembly quality and coverage metrics change with sequencing depth.
Show command line
sequana_lora \ --assembler flye \ --input-directory streptococcus/ \ --mode bacteria \ --data-type pacbio-hifi \ --genome-size 2m \ --apptainer-prefix /home/cokelaer/images \ --checkm-rank genus \ --checkm-name Streptococcus \ --working-directory flye_10_bis \ --force --monitor \ --busco-lineage bacteria \ --busco-db-version odb10 \ --blast-remote-db nt \ --blast-email thomas.cokelaer@pasteur.fr
Versions: sequana_lora 1.0.1 · sequana 0.20.0 · sequana_pipetools 1.5.3 · Python 3.10.14
HTML Report Examples
⚙️ How to Use This Pipeline
Install sequana_lora and run on your own data:
1. Install
pip install sequana-lora
2. Initialize workflow
sequana_lora \ --assembler flye \ --input-directory /path/to/long_reads/ \ --data-type pacbio-hifi \ --genome-size 2m \ --working-directory lora_output
3. Run with Snakemake
cd lora_output snakemake -c 8 # Use as many cores as needed
For more options (different assemblers, BUSCO, BLAST, etc.), see the GitHub README or Sequana documentation.
Resources: GitHub · Documentation · Sequana Docs · Test Data