Anthropological long-read analysis for ascorbate-pathway signals, nutritional stress, older remains, historical samples, and intergenerational research contexts.
Upload FASTQ/FASTQ.GZ for base QC, VCF for ascorbate-panel variant screening, bedMethyl/TSV for modified-base summaries, mosdepth coverage outputs, and mapDamage/schmutzi/PMDtools-style authentication reports, and external workflow summaries from fastVEP, LongHap/LongPhase, wf-human-variation, PastForward, Mapache, aMeta, Sniffles2, cuteSV, or MultiQC. BAM/SAM are registered for CLI pipeline processing.
ADLA evaluates genomic, modified-base, preservation, and contextual evidence relevant to ascorbate stress and scurvy-like vulnerability in anthropological, historical, ancient-remains, and intergenerational research. It does not diagnose vitamin C deficiency or scurvy.
Bundled seed windows are active immediately. For full coverage/callability, generate data/target_panels/adla_full_gene_targets.GRCh38.generated.bed from GENCODE/RefSeq using scripts/generate_target_bed.php.
ADLA separates sequence-derived signals from anthropological interpretation. Variant, methylation, and coverage results are treated as research evidence only when preservation, sample material, contamination, osteological, isotopic, ecological, and historical context are documented.
Older remains require authentication review. Fragment length alone is descriptive; deamination/damage, contamination controls, provenance, extraction/library records, and target callability must be assessed before pathway inference.
Direct ONT modified-base calls from native DNA are not equivalent to ancient DNA methylation reconstruction from damage/deamination. The report gates methylation language by sample age and metadata completeness.