Purdue University

Snap is a semi-HMM-based Nucleic Acid Parser -- gene prediction tool.

Snap-aligner (Scalable Nucleotide Alignment Program) is a fast and accurate read aligner for high-throughput sequencing data.

Snaptools is a python module for pre-processing and working with snap file.

Snippy is a tool for rapid haploid variant calling and core genome alignment.

Snp-dists is a tool to convert a FASTA alignment to SNP distance matrix.

SNP-sites is a tool that apidly extracts SNPs from a multi-FASTA alignment.

Snpeff is an open source tool that annotates variants and predicts their effects on genes by using an interval forest approach.

Snpgenie is a collection of Perl scripts for estimating ?N/?S, dN/dS, and gene diversity from next-generation sequencing (NGS) single-nucleotide polymorphism (SNP) variant data.

Snphylo is a pipeline to generate a phylogenetic tree from huge SNP data.

Snpsift is a tool used to annotate genomic variants using databases, filters, and manipulates genomic annotated variants.

Soapdenovo2 is a short-read assembly method to build de novo draft assembly.

SortMeRNA is a local sequence alignment tool for filtering, mapping and clustering.

souporcell is a method for clustering mixed-genotype scRNAseq experiments by individual.

Sourmash is a tool for quickly search, compare, and analyze genomic and metagenomic data sets.

Spaceranger is a set of analysis pipelines that process Visium Spatial Gene Expression data with brightfield and fluorescence microscope images.

SPAdes - St. Petersburg genome assembler - is an assembly toolkit containing various assembly pipelines.

Apache Spark is a fast and general engine for large-scale data processing.

SPECFEM3D Cartesian simulates acoustic fluid, elastic solid, coupled acoustic/elastic, poroelastic or seismic wave propagation in any type of conforming mesh of hexahedra structured or not. It can, for instance, model seismic waves propagating in sedimentary basins or any other regional geological model following earthquakes. It can also be used for non-destructive testing or for ocean acoustics.

SPECFEM3D Globe simulates global and regional continental-scale seismic wave propagation.

Sprod: De-noising Spatially Resolved Transcriptomics Data Based on Position and Image Information.