Purdue University

Seqkit is a rapid tool for manipulating fasta and fastq files.

Seqyclean is used to pre-process NGS data in order to prepare for downstream analysis.

SHAPEIT4 is a fast and accurate method for estimation of haplotypes (aka phasing) for SNP array and high coverage sequencing data.

SHAPEIT5 is a software package to estimate haplotypes in large genotype datasets (WGS and SNP array).

Shasta is a software for de novo assembly from Oxford Nanopore reads.

Shigeifinder is a tool that is used to identify differentiate Shigella/EIEC using cluster-specific genes and identify the serotype using O-antigen/H-antigen genes.

Shorah is an open source project for the analysis of next generation sequencing data.

Shortstack is a tool for comprehensive annotation and quantification of small RNA genes.

Shovill is a tool to assemble bacterial isolate genomes from Illumina paired-end reads.

Sicer is a clustering approach for identification of enriched domains from histone modification ChIP-Seq data.

Sicer2 is the redesigned and improved ChIP-seq broad peak calling tool SICER.

SignalP predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive prokaryotes, Gram-negative prokaryotes, and eukaryotes.

SignalP predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive prokaryotes, Gram-negative prokaryotes, and eukaryotes.

Simug is a general-purpose genome simulator.

SingleM is a tool for profiling shotgun metagenomes. It has a particular strength in detecting microbial lineages which are not in reference databases. The method it uses also makes it suitable for some related tasks, such as assessing eukaryotic contamination, finding bias in genome recovery, computing ecological diversity metrics, and lineage-targeted MAG recovery.

SKA (Split Kmer Analysis) is a toolkit for prokaryotic (and any other small, haploid) DNA sequence analysis using split kmers.

Skewer is a fast and accurate adapter trimmer for paired-end reads.

Slamdunk is a novel, fully automated software tool for automated, robust, scalable and reproducible SLAMseq data analysis.

Smoove simplifies and speeds calling and genotyping SVs for short reads.

Snakemake is a workflow engine that provides a readable Python-based workflow definition language and a powerful execution environment that scales from single-core workstations to compute clusters without modifying the workflow.