PJ Labs · macOS · local genomics
Your genome data. Your Mac. A professional report.
Genome is a native workbench for WGS data: from FASTQ, BAM and CRAM through HLA, KIR, LPA, pharmacogenetics, repeat expansions, SNP search, microarray exports and reference management to PDF-first reports. Without cloud and without upload.
App tour
What Genome feels like.
Every area of the app, cut out. Just swipe through.
Workflow
Presets, prerequisites, start actions and custom workflows in a calm native Mac interface.
Data management
Load BAM/CRAM, check paths, read status and manage inputs for all workflows in one place.
Conversion
Prepare, check, index and convert FASTQ, BAM and CRAM locally between formats.
Analysis
Run domain-specific evaluations for mtDNA, EBV, HLA, KIR, pharmacogenetics, repeats, LPA, PGS and microarray data.
Single-gene analysis
Select individual genes, inspect coverage and variants by category, and review technical details in one targeted workflow.
SNP search
Look up rsIDs in your own genotype data, normalize, enrich and inspect them in a table.
Reports
PDF-first reports with data basis, evidence, cautionary notes, TOC and reproducible provenance.
Tools
See and control installed tools, versions, sizes, sources, updates and removal.
References
Manage GRCh38/hs38d1, HLA*LA graph, IPD-KIR, T1K references, dbSNP/ClinVar and panels locally.
Log
Trace runs, heartbeats, progress, warnings and technical output.
Help
Structured help directly in the app and online at pjlabs.dev.
Settings
App language, report language, appearance, export behavior and developer options, calmly grouped.
Completeness
Genome isn't a single report generator, but a continuous local genome workbench.
Workflow
Built-in and custom presets start complete runs: FASTQ→BAM, microarray export, HLA/LPA/PGx/repeat analysis and PDF reports.
Data Management
Load BAM/CRAM, check the index, read coverage/chromosome profile, open folders, copy paths and find artifacts again.
Conversion
Trim, align, sort and mark FASTQ, convert BAM↔CRAM, lift VCF, extract regions and build indexes.
Analysis
Domain-specific evaluations instead of a dashboard mix: mtDNA, EBV, HLA, KIR, Aldy, ExpansionHunter, KILDA, PGS, VCF and microarray.
Single-Gene Analysis
Targeted evaluation of individual genes from BAM/CRAM: per-gene coverage (share ≥20×), variants by category, coverage/quality traffic light and expandable technical details; selection via search, presets and categories.
SNP Search
Clean up rsID lists, search your own genotype files (Genome, MTHFR Genetics), normalize genotypes and show coverage/confidence. Built-in panels for vitamins A-E, antioxidant enzymes, vitamin D, lactose/caffeine, iron, detox, sports, sleep and pharma.
Reports
Genomic evaluations and pharmacogenetics as the primary PDF output; HTML remains a technical export.
Tools
Install, update, uninstall, version and validate Conda, Homebrew and Genome-managed tools.
References
Check the reference library, bundles, HLA*LA graph, IPD-KIR/T1K resources, database status and tool smoke tests.
Logs
Operations, errors, heartbeats, progress, quiet phases and technical output stay traceable.
Help
Structured help directly in the app and online, with searchable features and local explanations.
Settings
App language, report language, appearance, export behavior and developer options, calmly grouped.
Workflows & domains
Every function stays where it belongs technically, with its own inputs, tool limits and handoff into reports.
FASTQ → BAM/CRAM
fastp · bwa · samtools · mosdepth
Paired FASTQs are trimmed, aligned with bwa/bwa-mem2 or minimap2, sorted, marked-duplicated, indexed and logged with coverage/flagstat checks.
BAM/CRAM → Microarray
Genome · Genome Deep · Build 37/38
Genome produces three genotype formats from the WGS: Genome (all called SNPs), Genome Deep (for more info: additionally read depth and confidence per call) and MTHFR Genetics; a Genome provenance header and build 37/38 stay consistent.
Microarray deep mode
Genome Deep · AD/DP · Confidence
Beyond the genotype, Genome writes per-SNP allele depths (AD/DP), allele balance and a confidence (homozygous, heterozygous or not callable) into the Genome Deep file. A header line summarises how many positions are confidently called.
HLA*LA + T1K
HLA*LA · T1K · IMGT/HLA
HLA*LA provides G-groups, coverage, Q1/Q2 and DRB hints. T1K adds HLA/KIR as a second technical evidence layer and makes concordance visible.
KIR / T1K
KIR · IPD-KIR · T1K
KIR genes and KIR-HLA context are kept separate from the HLA block, with IPD-KIR reference, technical evidence and a clear gene/allele view.
LPA / KILDA
KILDA · LPA · KIV-2
KILDA/KIV-2 context is treated as its own module. Raw values like quantile=NA stay visible instead of appearing as a deceptively smooth interpretation.
Aldy / Pharmacogenetics
Aldy 4 · PharmCAT · CPIC/DPWG
Aldy 4 handles complex PGx genes; PharmCAT/SNP rules add variant context. Aldy stays strictly pharmacogenetics-only. Results are for research and education, not for guiding medication or dosing.
ExpansionHunter
Repeat · STR · ExpansionHunter
Repeat loci, allele sizes, read evidence and confidence intervals are rendered per upstream semantics, separate from small-variant genotypes.
mtDNA, Y, EBV & Microbiome
Haplogrep 3 · EBV · Kraken2
mtDNA and Y artifacts, Haplogrep 3, EBV coverage/VCF and optional Kraken2/Bracken contexts stay recognizable as technical evidence.
PGS & SNP context
PGS Catalog · rsID · ClinVar
PGS Catalog files, individual rsIDs, APOE/BRCA/HFE/F5/CYP examples and your own SNP files are evaluated locally and placed in context.
Single gene analysis
bcftools · mosdepth · ClinVar
Targeted evaluation of individual genes from BAM/CRAM: per-gene coverage (share of bases ≥20×) and variants, grouped by category, with a coverage/quality traffic light and expandable technical details. Selection via search, presets and categories.
Toolchain
Genome wraps bioinformatics, but doesn't hide it.
The Tools page shows paths, versions, sizes, updates and validation. Installing and uninstalling covers the usual alignment tools as well as KILDA, Aldy, ExpansionHunter, T1K, HLA*LA and references.
Core Alignment
fastp · fastqc · bwa/bwa-mem2 · minimap2 · samtools · sambamba · mosdepth · pigz
Variant & Utility
bcftools · tabix/bgzip · bedtools · Java · Picard · Python 3 · kallisto
Specialized Genomics
HLA*LA · T1K · KILDA · Nextflow · jellyfish · Aldy 4 · ExpansionHunter · Haplogrep 3
Optional Context
Kraken2 · Bracken · dbSNP · ClinVar · PGS Catalog · Genome+ Microarray Panels
Reports
PDF is the primary output, with clean evidence instead of marketing scores.
Genomic evaluations
HLA, T1K-HLA/KIR, KILDA/LPA, repeat expansions, SNP/ClinVar context, PGS, mtDNA/Haplogrep and technical evidence only appear when matching inputs are actually present.
Pharmacogenetics
PGx stays PGx: Aldy diplotypes, PharmCAT/SNP rules, CPIC/DPWG/PharmGKB context and cautious language without mixing in HLA/KIR raw appendices. For research and education, not for individual medication, dosing or treatment decisions.
Report modules
HLA & T1K concordance · KIR / T1K · Pharmacogenetics & Aldy · LPA / KILDA · Repeat expansions · SNP/ClinVar/PGS context · mtDNA/Haplogrep · EBV & technical evidence
Local and traceable
No cloud, no account, no upload. Paths, versions, inputs, references, manifests and logs stay visible.
No false simplification
Genome separates raw value, tool limit, technical evidence, context and cautious interpretation.
Apple-native interface
SwiftUI, system color, sidebar, compact controls, PJDesignKit typography and calm cards instead of a web dashboard.
Download
Try Genome on your Mac.
Local data processing, structured help, professional reports and a toolchain that stays visible.
Intended use
Research Use OnlyFor research and education, not a medical device or IVD.
Genome is a software tool for the local, technical processing and exploration of genomic raw data (FASTQ, BAM, CRAM, VCF, microarray) on your own Mac. It is aimed at researchers, bioinformaticians and technically minded people who examine their own data for scientific or educational purposes.
Genome is intended exclusively for research, informational and educational use (Research Use Only). Unless expressly stated otherwise, it is not a medical device and not an in-vitro diagnostic within the meaning of the applicable EU medical device and in-vitro diagnostic regulations, including MDR and IVDR. It is not intended to detect, diagnose, predict, monitor, prevent or treat any disease or health condition, nor to guide clinical, therapeutic or medication-dosing decisions.
Its outputs are technical evaluations and annotations from public databases, not a medical finding, not a diagnosis, not an exclusion and not individual medical advice. For health-related questions or genetic analyses for medical purposes, please consult a qualified professional (e.g. a specialist in medical genetics).