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SaffronTree: Reference free rapid phylogenetic tree construction from raw read data

SaffronTree: Reference free rapid phylogenetic tree construction from raw read data

SAIGE is an R package with Scalable and Accurate Implementation of Generalized mixed model (Chen, H. et al. 2016). It accounts for sample relatedness and is feasible for genetic association tests in large cohorts and biobanks (N > 400,000).

Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

Salsa is a tool to scaffold long read assemblies with Hi-C.

Tools for working with SAM/BAM data

Processes haplotag barcodes in SAM format.

Plot structural variant signals from BAMs and CRAMs.

Tools for dealing with SAM, BAM and CRAM files

SAP makes statistical assingment of an unknown DNA sequence to taxa represented by sequences in GenBank. Each assignment is associated with a posterior probility that serve as a confidence in the assignment.

Single-Cell Analysis in Python. Scales to >1M cells.

A Python package for exploring and analysing genetic variation data.

Scipion 3 (alpha)

Screen is a full-screen window manager that multiplexes a physical terminal between several processes, typically interactive shells

a cross-platform and ultrafast toolkit for FASTA/Q file manipulation

Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format

fast and accurate method for estimation of haplotypes (phasing)

a computer program for refining a model of isomorphous heavy-atom substitution and calculating phase probabilities from it

Rapidly produce accurate assembled sequence using as input DNA reads generated by Oxford Nanopore flow cells.

ShortStack: Comprehensive annotation and quantification of small RNA genes

A clustering approach for identification of enriched domains from histone modification ChIP-Seq data

Redesigned and improved ChIP-seq broad peak calling tool SICER.

retrieving data from OAI interfaces the Pythonic way:

Windowed Adaptive Trimming for fastq files using quality

SIFT 4G is a faster version of SIFT that enables us to scale up and provide SIFT predictions for more organisms.

The SignalP 5.0 server predicts the presence of signal peptides and the location of their cleavage sites in proteins from Archaea, Gram-positive Bacteria, Gram-negative Bacteria and Eukarya.

Simka and simkaMin are de novo comparative metagenomics tools. Simka represents each dataset as a k-mer spectrum and computes several classical ecological distances between them. SimkaMin outputs approximate (but very similar) results by subsampling the kmer space and requires much less computational resources.

a program package for cryo-EM image processing, focusing on ab initio 3D reconstruction of low-symmetry single-particles

open source, container solution for compute based workloads

Forward-time population genetics simulator

SLR is a scaffolding tool based on long reads and contig classification

Ultra-fast de novo assembler using long noisy reads

smoove simplifies and speeds calling and genotyping SVs for short reads. It also improves specificity by removing many spurious alignment signals that are indicative of low-level noise and often contribute to spurious calls.

A popular workflow management system aiming at full in-silico reproducibility.

Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data

Sniffles is a structural variation caller using third generation sequencing (PacBio or Oxford Nanopore)

Rapid bacterial SNP calling and core genome alignments

Finds SNP sites from a multi-FASTA alignment file.

Genetic variant annotation and effect prediction toolbox

Toolbox that allows you to filter and manipulate annotated files

SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes.

calculates sequence quality statistics and creates visual representations of data quality for second-generation sequencing data

SonicParanoid: fast, easy and accurate orthology inference

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

Space Ranger is a set of analysis pipelines that process Visium spatial RNA-seq output and brightfield and fluorescence microscope images in order to detect tissue, align reads, generate feature-spot matrices, perform clustering and gene expression analysis, and place spots in spatial context on the slide image.

SPAdes (St. Petersburg genome assembler) is intended for both standard isolates and single-cell MDA bacteria assemblies.

Map and align a set of cDNA/EST or protein sequences onto a genome

SparCC is a python module for computing correlations in compositional data (16S, metagenomics, etc).

a spectral learning algorithm for hidden Markov models for epigenomic data

Implements a self-contained, zero-configuration, SQL database engine

SqueezeMeta: a fully automated metagenomics pipeline, from reads to bins

An SRA tool identifies and removes any significant human read, and outputs the edited (cleaned) fastq file for SRA submission.

SRA Toolkit and SDK from NCBI

SRPRISM - Short Read Alignment Tool

Stacks is a software pipeline for building loci from RAD-seq

Staden package - A fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin)

An RNA-seq read aligner.

STREAM Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data http://stream.pinellolab.org

Strelka calls somatic and germline small variants from mapped sequencing reads

StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.

The program structure is a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. It can be applied to most of the commonly-used genetic markers, including SNPS, microsatellites, RFLPs and AFLPs.

High-performance read alignment, quantification, and mutation discovery

Fast and exact comparison of sequences

A robust and fast clustering method for amplicon-based studies.