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 it feels like to click through Genome.
Pick an app area on the left. The real cut-out screenshot window switches just like a click inside the app.
Workflow
Presets, prerequisites, start actions and custom workflows in a calm native Mac interface.
Completeness
Genome isn't a single report generator, but a continuous local genome workbench.
Workflow
Built-in and custom presets run complete pipelines: 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.
SNP search
Clean up rsID lists, search CombinedKit/23andMe/Ancestry data, normalize genotypes and show coverage/confidence.
Reports
Medical genomics 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.
Log & help
Operations, errors, quiet phases, search hits, online help and local explanations stay findable.
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
CombinedKit · 23andMe · Build 37/38
Genome produces 23andMe, AncestryDNA, FTDNA, Living DNA, MyHeritage, GEDmatch and CombinedKit; headers and build 37/38 stay consistent.
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.
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.
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.
Medical genomics
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.
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.