PJ Labs · macOS · local genomics
Explore genome data.On your Mac.
From sequencing reads to individual variants and PDF reports. A local workbench for research and education.
What you can do
Which files do you already have?
FASTQ reads
Start with the paired files from sequencing. Prepare and align reads before investigating variants.
BAM or CRAM
Your reads are already aligned. Check coverage, search for an rsID directly in a BAM or examine individual genes.
Genotype file
Load a supported genotype file and inspect the variants it contains. Available analyses depend on the file format and data.
A closer look
One rsID. Straight to your BAM.
Search for rs numbers in your BAM file with Genome. Inspect the genotype together with read support and quality, without exporting a genotype file first.
Read the step-by-step guideAnalyses in detail
Choose the analysis that fits your data.
01 Prepare sequencing reads
Start with paired FASTQ files. Genome aligns the reads to a reference genome and creates sorted, indexed BAM/CRAM files with quality information.
02 Export genotype files
Create genotype files from aligned sequencing data. Choose Genome, Genome Deep or the MTHFR Genetics format to match the next processing step.
03 Inspect read support
Genome Deep includes allele depths and confidence information alongside the genotype. This helps distinguish supported calls from positions that cannot be assessed.
04 HLA typing
Estimate HLA types from suitable sequencing data using HLA*LA and T1K. Inspect coverage, ambiguous assignments and agreement between the tools.
05 KIR analysis
Examine KIR genes and alleles with T1K. KIR results and their relationship to HLA are presented separately from HLA typing.
06 LPA repeat analysis
Use KILDA to examine the KIV-2 repeat region in LPA. Technical values and unavailable results remain visible for interpretation.
07 Pharmacogenetics
Examine selected pharmacogenetic genes with Aldy and variant annotations. Results are for research and education, not for medication or dosing decisions.
08 Repeat expansions
Examine supported repeat loci with ExpansionHunter. Review estimated allele sizes together with read evidence and confidence intervals.
09 Additional sequencing analyses
Explore mitochondrial and Y-chromosome data, EBV reads or optional microbiome analyses. Each module requires suitable input data and references.
10 SNPs and score context
Search for individual rsIDs directly in BAM files or work with PGS Catalog data. Results depend on the available variants, coverage and the requirements of each analysis.
11 Individual genes
Select a gene from your BAM/CRAM data. Review its coverage, variants and quality information together in one focused view.
Show analysis tools
Genome uses specialist bioinformatics tools for each task. You can inspect their versions and installation status in the app.
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
App tour
A look inside the app.
Browse the views for data management, analysis and reports.
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 reports with data sources, quality information and a table of contents.
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
Follow the progress, warnings and technical output of each run.
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.
Reports
Results with their data basis and limitations.
Data basis and quality
PDF reports bring together the analyses available for your files. Sources, quality information and technical limitations help you interpret each result. A missing or uncertain result is not evidence of absence.
Pharmacogenetics
Pharmacogenetic results form a separate section, with their own sources and limitations. They are for research and education, not for deciding on medication, doses or treatment.
Report modules
HLA & T1K concordance · KIR / T1K · Pharmacogenetics & Aldy · LPA / KILDA · Repeat expansions · SNP/ClinVar/PGS context · mtDNA/Haplogrep · EBV & technical evidence
Getting started
Load. Analyse. Review.
01
Load your files
Start with paired FASTQ files, an existing BAM/CRAM or a supported genotype file.
02
Prepare the analysis
Select a workflow and check the required tools, references and input quality.
03
Review the results
Inspect the output and log, then create a report from the available analyses.
Before you start
What you need.
A compatible Mac
Genome requires macOS 26 Tahoe or later and Apple Silicon. Allow additional storage for reference data and intermediate files.
Suitable input data
The available analyses depend on file type, reference build and coverage. A genotype file does not provide the same information as whole-genome sequencing.
Time for setup
Tools and reference data must be downloaded before the relevant analysis can run. Setup and processing time depend on the selected workflow and your Mac.
Download
Ready to work with your files?
The download page includes the current version and installation instructions. The help explains how to prepare your first analysis.
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).