Falco 1.3.0 Windows port
Quality control tool for raw RNA-seq reads. FastQC alternative.
Most NGS (Next-Generation Sequencing) analysis tools are built for Linux or macOS, and native Windows binaries have been hard to come by. Win-NGS distributes Windows binaries of standard NGS analysis tools built with no or minimal code modifications — STAR, fastp, bedtools and more — as well as original tools developed by our lab, so you can run NGS workflows natively on Windows. The site also collects curated links to other Windows-native NGS analysis software.
Basic RNA-seq Tools for Windows
A minimal toolchain for running RNA-seq analysis natively on Windows.
STAR 2.7.11b-r4 Windows port
Splice-aware aligner for short RNA-seq reads.
winget install WinNGS.STAR
featureCounts Repack
Per-gene read counter. The download link contains only featureCounts.exe.
winget install WinNGS.featureCounts
FlashDEG 1.1.0 Original
Fast, lightweight alternative to DESeq2 for differential expression analysis.
winget install WinNGS.FlashDEG
More Windows Builds & Bundles provided by Win-NGS
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 Windows port
Provides ultrafast preprocessing and quality control for FastQ data.
Read Alignment
minimap2 2.31 Windows port
Long-read sequence aligner for PacBio and Nanopore reads.
BWA-MEM2 2.3 Windows port
Short-read aligner for genome sequencing, ATAC-seq, ChIP-seq, etc.
Bowtie 2 2.5.5 Windows port
Short-read aligner for genome sequencing, ATAC-seq, ChIP-seq, etc.
HISAT2 2.2.2 Windows port
Splice-aware aligner for RNA-seq. Low memory requirements.
Read Quantification
kallisto 0.52.0 Windows port
Pseudoalignment-based transcript quantification from RNA-seq reads.
iso2gene 1.0.0 Original
Windows-native tool for tximport-style transcript-to-gene aggregation. Bridges kallisto output to FlashDEG.
StringTie 3.0.3 Windows port
Reference-guided transcript assembly and quantification from RNA-seq alignments.
BAM / VCF / BED Utilities
samtools 1.23.1 Repack
SAM/BAM/CRAM file manipulation — sorting, indexing, viewing, filtering. Standalone bundle including the required runtime DLLs.
bcftools 1.23.1 Repack
VCF/BCF manipulation, filtering, and variant calling. Includes plugins and the runtime DLLs needed to run standalone on Windows.
htslib 1.23.1 Repack
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 Windows port
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 NGS Tools
Third-party NGS tools that run on Windows out of the box or ship an official Windows installer.
Read Processing
SRA Toolkit
NCBI's toolkit for downloading SRA archives and converting them to FASTQ (
prefetch, fasterq-dump). Official Windows binary.
FastQC
Read quality checks. Java-based. Falco is a Windows-native alternative.
Trimmomatic
Read trimming. Java-based. Fastp is a Windows-native alternative.
SeqKit
FASTA/Q manipulation — stats, filtering, conversion, sorting. Official Windows binary.
Alignment & Downstream
Common NGS Tools Without Native Windows Support
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.
Frequently Asked Questions about NGS on Windows
Can you run NGS analysis on Windows?
Yes. Win-NGS provides self-compiled native Windows binaries for core NGS (Next-Generation Sequencing) tools such as STAR, fastp, samtools, bcftools, bedtools, minimap2, BWA-MEM2, HISAT2, kallisto and StringTie, so you can build a complete RNA-seq or DNA-seq workflow on Windows.
Do I need WSL to run NGS tools on Windows?
No. Every Win-NGS build runs natively on Windows without the Windows Subsystem for Linux (WSL). The binaries are compiled with MSYS2 (MSYS or UCRT64) and bundled with the runtime DLLs they need, so they run standalone.
Which NGS tools have native Windows builds?
Win-NGS distributes native Windows builds of Falco, STAR, featureCounts, fastp, minimap2, BWA-MEM2, kallisto, HISAT2, StringTie, samtools, bcftools, htslib and bedtools, plus links to other Windows-native tools like SeqKit, Bowtie2, IGV and the SRA Toolkit.
Are the Win-NGS Windows binaries free to use?
Yes. All binaries are free and distributed in accordance with the respective upstream open-source licenses. Review each tool's upstream license before use.
About this site
Win-NGS is a community portal for running NGS (Next-Generation Sequencing) analysis natively on Windows. 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.