ONT_PIPELINE

ONT pipelines for alignment, human-variation analysis, structural variants, and tandem repeats.

Alignment and human variation

Submit alignment with a directory containing ONT FASTQ files:

sbatch ont_alignment.sh \
  --sample-dir /path/to/fastq_directory \
  --reference /path/to/reference.fasta \
  --output-dir /path/to/output \
  --threads 16

After alignment finishes, submit human-variation analysis with its BAM output:

sbatch ont_human_variation.sh \
  --bam /path/to/aligned.bam \
  --output-dir /path/to/output

The reference defaults to human_GRCh38_no_alt_analysis_set.fasta on the Dashnow lab filesystem. Run bash ont_human_variation.sh --help for optional reference, sample, calling, region, and workflow settings.

Run the primary SV/TR workflows from the repository root, for example:

Catalog builder:

mkdir -p /pl/active/dashnowlab/software/ONT_PIPELINE/catalogs/TRExplorer.repeat_catalog_v2.hg38.1_to_1000bp_motifs.atarva.bed.gz.tmp/logs

sbatch -J annotsv_catalog -p acpu --qos=cpu-normal --time=23:00:00 --mem=2G
--output=logs/%x_%j.out --error=logs/%x_%j.err
--wrap="bash run_pipeline_slurm.sh annotate_bed.nf
--input_bed /pl/active/dashnowlab/projects/1k_tr_paper/data/TRExplorer.repeat_catalog_v2.hg38.1_to_1000bp_motifs.atarva.bed.gz
--software_path /pl/active/dashnowlab/software/ONT_PIPELINE
--work_dir /pl/active/dashnowlab/software/ONT_PIPELINE/catalogs/TRExplorer.repeat_catalog_v2.hg38.1_to_1000bp_motifs.atarva.bed.gz.tmp
--batch_size 10000
--annotsv_mem_gb 4
--java_mem_gb 16
--java_heap_gb 12
-resume"

bash run_pipeline_slurm.sh long_read_sv.nf \
  --bam_list resources/samples/test_bam.list \
  --work_dir /path/to/output \
  --ref /path/to/reference.fasta

sbatch -J long_read_str -p acpu --qos=cpu-normal --time=23:00:00 --mem=2G \
  --output=logs/%x_%j.out --error=logs/%x_%j.err \
  --wrap="bash run_pipeline_slurm.sh long_read_str_v2.nf \
  --bam_list /pl/active/dashnowlab/software/ONT_PIPELINE/resources/samples/shaikh_bam.list \
  --work_dir /pl/active/dashnowlab/work/ealiyev/SVTR_Analysis/SHAIKH_STR_PATHO_PRECOMPUTED \
  --projectname SHAIKH_STR_PATHO_PRECOMPUTED \
  --ref /pl/active/dashnowlab/data/ref-genomes/human_GRCh38_no_alt_analysis_set.fasta \
  --software_dir /pl/active/dashnowlab/work/ealiyev/SVTR_Analysis/software \
  --annotation_mode precomputed \
  --preannotated_tsv /pl/active/dashnowlab/software/ONT_PIPELINE/catalogs/TRExplorer.repeat_catalog_v2.hg38.1_to_1000bp_motifs.atarva.annotated.subset.tsv \
  -resume"

Repository-owned paths are resolved relative to this checkout. Python utilities are in scripts/, bundled datasets in resources/, usage examples in docs/, and superseded or experimental files in backup/.