1. Enviroment configuration

1.1 Official Images (Direct Download)

These tools have stable Docker images maintained by their own development teams or the community (BioContainers). Download them directly on HiPerGator using apptainer pull

# Create a directory to store your images
mkdir -p /blue/<your_group>/$USER/apptainer_images
cd /blue/<your_group>/$USER/apptainer_images

# Download FCS-GX (Targeted Contamination)
apptainer pull fcs-gx.sif docker://ncbi/fcs-gx:latest

# Download FCS-Adaptor (Adapter Trimming)
apptainer pull fcs-adaptor.sif docker://ncbi/fcs-adaptor:latest

# Download DeepPolisher (ML Polishing)
apptainer pull deeppolisher.sif docker://google/deeppolisher:latest

# Download BUSCO (Completeness)
apptainer pull busco.sif docker://ezlabgva/busco:v5.7.1_cv1

# Download BlobToolKit (Visual QC for Contamination)
apptainer pull blobtoolkit.sif docker://genomehubs/blobtoolkit:latest

1.2. Custom Modular Images

Lighter tools and dependencies for custom scripts (Python/R) are grouped into three specific modules. The definition files (.def) for these modules are located in the repository.

Module A (qc_env.sif): Read QC, filtering, and R-based Flow Cytometry analysis (fastqc, seqkit, trimmomatic, R tidyverse).

Module B (assembly_env.sif): Core assembly and alignment (hifiasm, minimap2, samtools, bwa).

Module C (curation_env.sif): Scaffolding, gap-filling, and structural curation (HapHiC, inspector, nextpolish2, TGS-GapFiller).

To build these custom images on the cluster without root privileges, use the --fakeroot flag. For example, to build Module A:

apptainer build --fakeroot qc_env.sif qc_env.def

2. Assembly Pipeline

2.1. Pre processing

HiFi BAM to fastq

Coverage Calculator