#1974 Add CRAM + mini reference for HG002 ONT telomere test data Pull request opened by pinin4fjords Summary • Add a CRAM version of

HG002_ont_tel_sub.bam

(17 ONT telomeric reads from GIAB HG002) • Include a compact mini reference FASTA (~149 KB) covering the telomeric ends of chr1 and chr2 from GRCh38 • This enables CRAM input testing for nf-core modules (telogator2, telomerehunter) without requiring the full 3 GB GRCh38 reference The CRAM preserves all 17 original reads with coordinates adjusted to the mini reference. Read sequences and qualities are identical to the BAM. New files | File | Size | Description | | ---------------------------- | ------ | ----------------------------------------- | | HG002_ont_tel_sub.cram | 309 KB | CRAM with adjusted coordinates | | HG002_ont_tel_sub.cram.crai | 66 B | CRAM index | | HG002_ont_tel_sub_ref.fa | 149 KB | Mini reference (chr1: 56 kb, chr2: 94 kb) | | HG002_ont_tel_sub_ref.fa.fai | 42 B | Reference index | How the CRAM was generated 1. Extracted the last ~56 kb of chr1 and ~94 kb of chr2 from GRCh38 into a mini reference 2. Rewrote BAM coordinates using pysam (subtracting region offsets) 3. Converted to CRAM using the mini reference Test plan • Verified CRAM contains all 17 reads (same as BAM) • Verified read sequences and lengths match the BAM • Verified CRAM is readable with

samtools view -T HG002_ont_tel_sub_ref.fa

• Tested with telogator2 nf-core module (same cluster results as BAM input) 🤖 Generated with Claude Code nf-core/test-datasets