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.
Job: adla_20260707_070526_d0551175 · 2026-07-07T07:05:26+00:00
| Domain | Status | Summary |
|---|---|---|
| genomic susceptibility | not observed in uploaded inputs | 0 curated ascorbate-transporter hit(s); 0 target-window variant(s). |
| modified base or methylation signal | not available | 0 target methylation/modified-base summary row(s). |
| ancient dna authenticity | not required for modern context | Age class: unknown; material: unknown; imported authentication reports: 1. |
| authentication imports | structured authentication evidence imported | Tools: schmutzi; flags: low_contamination_estimate, damage_metric_present, pmd_metric_present, endogenous_fraction_present |
| osteological paleopathology | not provided | |
| isotopic dietary context | not provided | |
| historical ethnographic context | not provided | |
| ecological or provisioning constraint | not provided | |
| intergenerational context | not specified |
No FASTQ fragment profile available. Upload FASTQ or attach an external damage/fragment report in notes.
| Metric | Count | Min | Mean | Max | Unit |
|---|---|---|---|---|---|
| contamination percent | 1 | 2.4000 | 2.4000 | 2.4000 | percent |
| mitochondrial contamination percent | 1 | 2.8000 | 2.8000 | 2.8000 | percent |
| nuclear contamination percent | 1 | 1.9000 | 1.9000 | 1.9000 | percent |
| endogenous fraction percent | 1 | 47.3000 | 47.3000 | 47.3000 | percent |
| c to t 5prime percent | 1 | 14.2000 | 14.2000 | 14.2000 | percent |
| g to a 3prime percent | 1 | 11.7000 | 11.7000 | 11.7000 | percent |
| damage percent | 1 | 12.9000 | 12.9000 | 12.9000 | percent |
| mean pmd score | 1 | 0.8700 | 0.8700 | 0.8700 | score |
| pmd positive percent | 1 | 68.4000 | 68.4000 | 68.4000 | percent |
| median fragment length bp | 1 | 68.0000 | 68.0000 | 68.0000 | bp |
| mean fragment length bp | 1 | 79.5000 | 79.5000 | 79.5000 | bp |
| short fragment percent le100 | 1 | 72.1000 | 72.1000 | 72.1000 | percent |
| File | Tool guess | Status | Flags | Metrics | Messages |
|---|---|---|---|---|---|
| reich_lab_style_demo.auth.json | schmutzi | parsed structured metrics | low_contamination_estimate, damage_metric_present, pmd_metric_present, endogenous_fraction_present |
contamination percent:
2.4000 percent mitochondrial contamination percent: 2.8000 percent nuclear contamination percent: 1.9000 percent endogenous fraction percent: 47.3000 percent c to t 5prime percent: 14.2000 percent g to a 3prime percent: 11.7000 percent damage percent: 12.9000 percent mean pmd score: 0.8700 score pmd positive percent: 68.4000 percent median fragment length bp: 68.0000 bp mean fragment length bp: 79.5000 bp short fragment percent le100: 72.1000 percent |
parsed
Structured JSON authentication/QC report was parsed. supporting Imported contamination estimate is low (2.8%), subject to tool assumptions and sample context. supporting Damage/deamination-style metric imported from schmutzi. supporting PMD-style authenticity metric imported from schmutzi. context Endogenous DNA fraction metric imported. review Parse assumptions were recorded. Verify extracted metrics against the original authentication report before publication-quality interpretation. Parse assumptions
|
No target-region variants were available for scoring. Upload a VCF with target-window hits or run the annotation pipeline first.
No direct FASTQ input was parsed. Use FASTQ/FASTQ.GZ for web-mode QC or NanoPlot from the CLI pipeline.
No curated rsID hits detected in parsed VCF files.
No unclassified target-window VCF hits were detected.
No VCF annotation fields were parsed yet. Upload a VEP/ClinVar/dbSNP-annotated VCF or run php scripts/run_pipeline.php --job=<job_id> --stage=annotation --execute.
No target-region ClinVar annotations were detected.
No target-region VEP HIGH/MODERATE annotations were detected.
No VEP consequence counts.
No ClinVar significance counts.
No target-region bedMethyl rows were parsed. Upload Modkit bedMethyl or run the CLI pipeline against modBAM.
No mosdepth/target coverage file was parsed. Run CLI coverage with the generated BED panel or upload a mosdepth regions BED/TSV.
No external workflow outputs were imported.
No external profile imports detected.
No fastVEP, LongHap/LongPhase, wf-human-variation, PastForward, Mapache, aMeta, MultiQC, Sniffles2, or cuteSV summary imports were parsed.
No target-region phased variants were detected. Upload phased VCFs or LongHap/LongPhase summaries.
No SV type counts.
No structural variants overlapped ADLA target windows. Upload Sniffles2/cuteSV VCFs for target overlap review.
No aMeta/KrakenUniq/MALT/MaltExtract microbial context imports were parsed.
Fast local VEP-compatible consequence and supplementary annotation import.
Mode: worker_or_import · Category: annotation
import readyUse as a fast local annotation path; VEP remains a conservative reference path.
Import or execute haplotype phasing that integrates long-read methylation evidence.
Mode: worker_or_import · Category: phasing
import readyHigh value for intergenerational and haplotype-context interpretation.
Co-phase SNPs, indels, SVs, and 5mC modifications from long reads.
Mode: worker_or_import · Category: phasing
import readyUseful for broad long-read haplotype context.
Import ONT workflow outputs for small variants, SVs, CNVs, STRs, modified bases, and phasing.
Mode: external_worker_import · Category: ont_reference_workflow
import readyToo heavy for shared hosting; import reports and derived VCF/bedMethyl outputs.
Import historical/ancient-DNA mapping, contamination, coverage, and damage-rescaling summaries.
Mode: external_worker_import · Category: ancient_dna_workflow
import readyStrengthens anthropological readiness and authenticity review.
Import ancient-DNA mapping/QC/imputation workflow summaries.
Mode: external_worker_import · Category: ancient_dna_workflow
import readySupports reproducible mapping context for older remains.
Import ancient microbiome/pathogen/burial-context summaries from aMeta/MALT/KrakenUniq/MaltExtract.
Mode: external_worker_import · Category: microbial_context
import readyContextual evidence only; useful for preservation, oral/gut/pathogen/burial signals.
Import long-read SV calls and compare target-window overlaps.
Mode: worker_or_import · Category: structural_variants
import readyCaller concordance is preferred before strong SV interpretation.
ONT basecalling, demultiplexing, alignment support, and modified-base calling from POD5/FAST5 inputs.
Path: tools/bin/dorado
License: Oxford Nanopore Technologies license; verify redistribution terms before bundling.
not installedSummarize modified-base BAM/modBAM into bedMethyl and per-region modification reports.
Path: tools/bin/modkit
License: Check upstream nanoporetech/modkit license before redistribution.
not installedLong-read QC plots and HTML summaries for FASTQ/BAM/sequencing_summary inputs.
Path: tools/bin/NanoPlot
License: MIT
not installedFast ONT read filtering by length, quality, and GC thresholds.
Path: tools/bin/chopper
License: MIT/Apache-style Rust ecosystem dependencies; verify upstream repository.
not installedLong-read alignment to reference genomes.
Path: tools/bin/minimap2
License: MIT-like; verify upstream LICENSE.txt.
not installedBAM/SAM sorting, indexing, and summary statistics.
Path: tools/bin/samtools
License: MIT/BSD-style; verify htslib/samtools license.
not installedFast BAM/CRAM depth summaries and target coverage/callability checks.
Path: tools/bin/mosdepth
License: MIT; verify upstream repository.
not installedLong-read germline small variant calling, including ONT models.
Path: tools/bin/run_clair3.sh
License: Check upstream HKU-BAL/Clair3 license and model terms.
not installedLong-read structural variant calling from ONT/PacBio alignments.
Path: tools/bin/sniffles
License: MIT; verify upstream repository.
not installedOffline/cache-based variant consequence annotation with transcript/protein effects, consequence terms, frequencies, and plugin support.
Path: tools/bin/vep
License: Apache 2.0 for Ensembl API code; data cache terms vary. Verify before redistribution.
not installedLocal VCF normalization, target slicing, indexing-aware filtering, and annotation transfer from ClinVar/dbSNP VCFs.
Path: tools/bin/bcftools
License: MIT/BSD-style htslib/samtools family; verify upstream version.
not installedIndex bgzip-compressed VCF/BED annotation files for local random access.
Path: tools/bin/tabix
License: MIT/BSD-style htslib/samtools family; verify upstream version.
not installedBlock gzip compression for VCF/BED files that need tabix indexing.
Path: tools/bin/bgzip
License: MIT/BSD-style htslib/samtools family; verify upstream version.
not installedAlternative local variant effect annotation when VEP cache is not installed.
Path: tools/bin/snpEff.jar
License: Verify current SnpEff license before redistributing jar files.
not installedAnnotate/filter VCFs using local ClinVar, dbSNP, dbNSFP, and other indexed files.
Path: tools/bin/SnpSift.jar
License: Verify current SnpSift/SnpEff license before redistributing jar files.
not installedOptional ClinVar XML-to-enhanced-VCF builder supporting GRCh37/GRCh38; useful if raw ClinVar VCF is insufficient for local interpretation workflows.
Path: tools/bin/clinvcf
License: Check upstream SeqOne/clinvcf license before redistribution.
not installedAncient DNA nucleotide misincorporation and fragmentation pattern assessment for authenticity/damage review.
Path: tools/bin/mapDamage
License: Check upstream license and dependencies before redistribution.
not installedPost-mortem damage score support for ancient DNA read filtering/authenticity workflows.
Path: tools/bin/pmdtools
License: Check upstream license before redistribution.
not installedMitochondrial contamination estimation and endogenous consensus support for ancient human DNA.
Path: tools/bin/schmutzi
License: Check upstream license and database terms before redistribution.
not installedAutosomal ancient-DNA contamination estimation using linkage disequilibrium breakdown; useful as an advanced nuclear-contamination context layer.
Path: tools/bin/contamLD
License: Check upstream Reich Lab/ContamLD terms before redistribution.
not installedGenotype-likelihood framework used in low-coverage and ancient DNA contexts, including chromosome-X contamination estimation workflows for applicable samples.
Path: tools/bin/angsd
License: Check upstream ANGSD license before redistribution.
not installedAncient DNA contamination estimation for male X-chromosome workflows; useful where applicable and when reference panels/metadata are appropriate.
Path: tools/bin/hapCon
License: Check upstream terms and reference-data requirements before redistribution.
not installedHigh-performance Rust variant consequence annotation with VEP-compatible outputs and supplementary database integration.
Path: tools/bin/fastvep
License: Check upstream fastVEP license and bundled database terms before redistribution.
not installedRead-based phasing that integrates native long-read methylation signals with variant calls.
Path: tools/bin/longhap
License: MIT per upstream repository at time of review; verify before redistribution.
not installedCo-phase SNPs, small indels, SVs, and 5mC modifications from Nanopore/PacBio long reads.
Path: tools/bin/longphase
License: GPL-3.0; verify upstream and redistribution requirements.
not installedEPI2ME Nextflow workflow for ONT human small variants, SVs, CNVs, STRs, modified bases, and phasing.
Path: tools/workflows/wf-human-variation
License: Check Oxford Nanopore/EPI2ME workflow terms and dependencies before redistribution.
not installedSnakemake pipeline for historical/ancient DNA processing, QC, contamination, coverage, and damage rescaling.
Path: tools/workflows/PastForward
License: MIT in current upstream repository; verify before redistribution.
not installedSnakemake ancient-DNA mapping workflow supporting reproducible mapping/QC/imputation context.
Path: tools/workflows/mapache
License: GPL-3.0; verify redistribution requirements.
not installedAncient metagenomic profiling workflow using trimming/QC, KrakenUniq, Bowtie2 pathogen screening, MapDamage2, MALT, and MaltExtract.
Path: tools/workflows/aMeta
License: Check upstream workflow and database terms before redistribution.
not installedLong-read structural variant caller for ONT/PacBio datasets; useful as an alternate/concordance SV caller with Sniffles2.
Path: tools/bin/cuteSV
License: Check upstream license before redistribution.
not installedK-mer-based taxonomic classification used in ancient metagenomic workflows such as aMeta.
Path: tools/bin/krakenuniq
License: Check upstream license and database terms.
not installedMEGAN Alignment Tool for metagenomic alignment/LCA workflows used in ancient microbial authentication.
Path: tools/bin/malt-run
License: Check upstream MEGAN/MALT terms.
not installedAuthentication and validation of microbial species detected in ancient metagenomic workflows.
Path: tools/bin/MaltExtract
License: Check upstream license and database terms.
not installedNo notes yet.
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.