Software Item | Details | ||||||
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spades | SPAdes – St. Petersburg genome assembler – is an assembly toolkit containing various assembly pipelines
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sparsehash | The Google SparseHash project contains several hash-map implementations in use at Google, with different performance characteristics, including an implementation that optimizes for space and one that optimizes for speed.
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spglib | Spglib is a library for finding and handling crystal symmetries written in C.
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spparks | sppakrs is a Monte Carlo program.
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sratoolkit | The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.
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stacks | Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform.
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stampy | a swiss-army knife of tools for a wide-range of genomics analysis tasks.
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star | Spliced Transcripts Alignment to a Reference
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starccm | Star-CCM+ is a CFD application that supports parallel processing.
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stata | Statistical analysis software.
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stata-mp | Statistical analysis software.
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strelka | Strelka is an analysis package designed to detect somatic SNVs and small indels from the aligned sequencing reads of matched tumor-normal samples.
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stringtie | StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.
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subread | a tool kit for processing next-gen sequencing data
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subversion | Apache Subversion centralized version control system.
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swig | SWIG is an interface compiler.
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szip | Szip is a compression library used with HDF5.
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tabix | A useful tool that indexes large .vcf files
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taco | Multi-sample transcriptome assembly from RNA-Seq
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tax2tree | The tax2tree software package was developed in collaboration with Greengenes for the purpose of transferring a taxonomy from one tree to another. Specifically, the motivation was to reduce the manual curation effort necessary for each release of Greengenes by automating the decoration of taxonomy.
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tecplot | Plotting and visualization software that gives full control over 2-D and 3-D plot parameters.
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thermocalc | software package for thermodynamic calculations
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tophat | TopHat is a program that aligns RNA-Seq reads to a genome in order to identify exon-exon splice junctions.
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torch | Torch is a scientific computing framework with wide support for machine learning algorithms.
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transdecoder | TransDecoder identifies candidate coding regions within transcriptsequences, such as those generated by de novo RNA-Seq transcript assemblyusing Trinity, or constructed based on RNA-Seq alignments to the genomeusing Tophat and Cufflinks.
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trilinos | Trilinos is an effort to develop algorithms and enabling technologies within an object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems.
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trimgalore | Consistent quality and adapter trimming for RRBS or standard FastQ files
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trimmomatic | Trimmomatic: A flexible read trimming tool for Illumina NGS data
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trinity | Trinity assembles transcript sequences from Illumina RNA-Seq data.
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twinscan | Twinscan gene-structure prediction
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uclust | UCLUST v1.2.22q (C) Copyright 2009-10 Robert C. Edgar.
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udunits | The UDUNITS-2 package provides support for units of physical quantities.
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unanimity | C++ library and its applications to generate and process accurate consensus sequences
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usearch | USEARCH offers search and clustering algorithms that are often orders of magnitude faster than BLAST.
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valet | This software is Open Source. almaBTE is a pipeline for detecting mis-assemblies in metagenomic assemblies.
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valgrind | Valgrind is an instrumentation framework for building dynamic analysis tools.
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vasp | [SPECIAL LICENSE REQUIRED: contact hpc-support@umich.edu] VASP, The Vienna Ab initio simulation package, a plane wave electronic structure code.
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vcfanno | Vcfanno provides fast, flexible annotation of genetic variants
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vcftools | VCFtools is a program package designed for working with VCF files, such as those generated by the 1000 Genomes Project. The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files.
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velvet | Velvet is a de novo genomic assembler specially designed for short read sequencing technologies such as Solexa or 454.
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Total pages: 13
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