Falco 1.3.0 (Win-NGS build)
Quality control tool for raw RNA-seq reads.
Most NGS (Next-Generation Sequencing) analysis tools are built with Linux or macOS in mind, and information about running them natively on Windows is scattered. This site collects tools that work on Windows out of the box, binaries we compiled ourselves, and links to useful external tools in one place.
Basic RNA-seq Tools
A minimal toolchain for running RNA-seq analysis natively on Windows. Self-built binaries, ready to run without WSL.
STAR 2.7.11b (Win-NGS build)
Splice-aware aligner for short RNA-seq reads.
featureCounts (redistribution)
Per-gene read counter. The download link contains only featureCounts.exe.
FlashDEG
Coming Soon
Cross-platform C/C++ implementation of DESeq2 for differential expression analysis. Win-NGS build coming soon.
More Windows Builds & Bundles
Additional NGS tools we have built or redistributed for Windows, grouped by function. "Build" entries are compiled from source with MSYS2; "Redistribution" entries repackage existing MSYS2 binaries together with the runtime DLLs needed to run standalone.
Read QC / Preprocessing
fastp 1.3.3 (Win-NGS build)
Provides ultrafast preprocessing and quality control for FastQ data.
Aligners & Quantification
minimap2 2.31 (Win-NGS build)
Versatile pairwise sequence aligner. The standard choice for long-read mapping (PacBio, ONT) and a fast option for short-read alignment.
BWA-MEM2 2.3 (Win-NGS build)
Faster reimplementation of BWA-MEM, the de facto standard short-read aligner. Suited for DNA-seq, ChIP-seq, and ATAC-seq workflows on Windows.
kallisto 0.52.0 (Win-NGS build)
Pseudoalignment-based transcript quantification from RNA-seq reads. Fast, alignment-free abundance estimates for downstream differential-expression workflows.
BAM / VCF / BED Utilities
samtools 1.23.1 (redistribution)
SAM/BAM/CRAM file manipulation — sorting, indexing, viewing, filtering. Standalone bundle including the required runtime DLLs.
bcftools 1.23.1 (redistribution)
VCF/BCF manipulation, filtering, and variant calling. Includes plugins and the runtime DLLs needed to run standalone on Windows.
htslib 1.23.1 (redistribution)
Core C library for high-throughput sequencing data formats (SAM/BAM/CRAM/VCF/BCF).
Ships the CLI utilities bgzip, tabix, htsfile,
and annot-tsv.
bedtools 2.31.1 (Win-NGS build)
Swiss-army knife for genomic interval operations — intersect, merge, sort, slop, coverage across BED / BAM / VCF / GFF.
Peak Calling
MACS (Windows patch)
Coming Soon
The most widely used peak caller for ChIP-seq and ATAC-seq. Win-NGS patched Windows build coming soon.
Other Windows-Native Tools
Third-party NGS tools that run on Windows out of the box or ship an official Windows installer.
Read Processing
FastQC
Read quality checks. Java-based; runs on Windows.
Trimmomatic
Adapter and low-quality base trimming. Java-based.
SeqKit
Swiss-army knife for FASTA/Q manipulation — stats, filtering, conversion, sorting. Statically linked Windows binary.
Alignment & Downstream
Bowtie2
Short-read aligner with official Windows binaries.
Picard Tools
SAM/BAM manipulation and metrics. Java-based.
SnpEff / SnpSift
Variant annotation. Java-based.
IGV (Integrative Genomics Viewer)
Visualizer for BAM/VCF/BED. Windows installer available.
bigtools
Rust-based BigWig/BigBed CLI — conversion, summary stats, merging. Official Windows binary.
Common Tools Not Supporting Windows
Widely-used NGS tools that do not run in a native Windows environment — whether because they are POSIX-only Python/Perl scripts or compiled tools with no Windows port. Use WSL2 or a Linux machine to run these.
GATK
The go-to variant calling toolkit. Java core with Linux-only native dependencies.
salmon
Fast and accurate transcript-level quantification from RNA-seq reads.
UMI-tools
Handling Unique Molecular Identifiers (UMIs): extraction, deduplication, grouping.
deepTools
Toolkit for exploring deep-sequencing data — coverage tracks, heatmaps, and visualization from BAM.
HISAT2
Splice-aware aligner for RNA-seq. The source compiles on Windows, but the bundled Perl wrapper scripts do not run correctly.
About this site
The source for this site is managed on GitHub. Please use issues and pull requests for additions and corrections to the tool listings.
Distributed binaries are provided in accordance with the respective upstream licenses. Please review the upstream license before using any binary listed here.