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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
https://github.com/nextstrain/auspice
Web application for visualizing pathogen evolution.Interactive web app for visualizing phylogenomic data.
Proper citation: Auspice (RRID:SCR_023966) Copy
https://github.com/sanger-pathogens/assembly-stats
Software to get assembly statistics from FASTA and FASTQ files.
Proper citation: assembly-stats (RRID:SCR_023963) Copy
https://github.com/thegenemyers/DEXTRACTOR
Software as Bax file decoder and data compressor.
Proper citation: DEXTRACTOR (RRID:SCR_024005) Copy
https://github.com/nexml/nexml.java
Software repository contains java code for NeXML processing.
Proper citation: Java NeXML libraries and tools (RRID:SCR_024084) Copy
The free Segway software package contains a novel method for analyzing multiple tracks of functional genomics data. The method uses a dynamic Bayesian network (DBN) model, which enables it to analyze the entire genome at 1-bp resolution even in the face of heterogeneous patterns of missing data. This method is the first application of DBN techniques to genome-scale data and the first genomic segmentation method designed for use with the maximum resolution data available from ChIP-seq experiments without downsampling. Segway uses the Graphical Models Toolkit (GMTK) for efficient DBN inference. The software has extensive documentation and was designed from the outset with external users in mind.
Proper citation: Segway - a way to segment the genome (RRID:SCR_004206) Copy
http://cudasw.sourceforge.net/
CUDASW++ is a bioinformatics software for Smith-Waterman protein database searches that takes advantage of the massively parallel CUDA architecture of NVIDIA Tesla GPUs to perform sequence searches 10x-50x faster than NCBI BLAST. In this algorithm, we deeply explore the SIMT (Single Instruction, Multiple Thread) and virtualized SIMD (Single Instruction, Multiple Data) abstractions to achieve fast speed. This algorithm has been fully tested on Tesla C1060, Tesla C2050, GeForce GTX 280 and GTX 295 graphics cards, and has been incorporated to NVIDIA Tesla Bio Workbench. * Operating System: Linux * Programming language: CUDA and C * Other requirements: CUDA SDK and Toolkits 2.0 or higher
Proper citation: CUDASW++ (RRID:SCR_008862) Copy
https://cran.r-project.org/package=psych
Software R package for multivariate analysis and scale construction using factor analysis, principal component analysis, cluster analysis and reliability analysis.Procedures for Psychological, Psychometric, and Personality Research. Used for personality, psychometric theory and experimental psychology.
Proper citation: psych (RRID:SCR_021744) Copy
https://metacpan.org/dist/Bio-ASN1-EntrezGene
Software regular expression based Perl Parser for NCBI Entrez Gene genome databases. Parses ASN.1-formatted Entrez Gene record and returns data structure that contains all data items from gene record.
Proper citation: Bio-ASN1-EntrezGene (RRID:SCR_024056) Copy
https://metacpan.org/dist/AcePerl
Software provides an interface to the ACEDB object-oriented database. Both read and write access is provided, and ACE objects are returned as similarly-structured Perl objects. Multiple databases can be opened simultaneously.
Proper citation: AcePerl (RRID:SCR_024057) Copy
http://bioinformatics.org/biococoa/
Open source framework for bioinformatics written in Objective-C. Provides Cocoa and GNUstep programmers with full suite of APIs for handling and manipulating biological sequences.
Proper citation: BioCocoa (RRID:SCR_023977) Copy
http://biblatex-biber.sourceforge.net/
Software bibliography processing backend for LaTeX biblatex package. Supports unsurpassed feature set for automated conformance to complex bibliography style requirements such as labelling, sorting and name handling. BibTeX replacement for users of BibLaTeX.
Proper citation: Biber (RRID:SCR_023973) Copy
Software Computer Assisted Medical Intervention Tool Kit helps researchers and clinicians to easily and rapidly collaborate in order to prototype CAMI applications, that feature medical images, surgical navigation and biomechanical simulations.Open source, cross-platform generic tool, written in C++, which can handle medical images, surgical navigations and biomechanical simulations.
Proper citation: CamiTK (RRID:SCR_023984) Copy
http://johnhommer.com/academic/code/aghermann
Sotware tool designed to run Process S simulations on Slow Wave Activity profiles from human EEG recordings.Produces set of sleep homeostat parameters which can be used to describe and differentiate individual sleepers, such as short vs long sleepers, early vs late, etc.Sleep research experiment manager, with facility for reading, displaying, and manual and semi-automatic scoring EEG recordings in edf format; conventional PSD and EEG Microcontinuity profiles; artifact detection; Independent Component Analysis; basic sleep analysis NREM-REM cycle detection.
Proper citation: Aghermann (RRID:SCR_023965) Copy
https://odelaneau.github.io/shapeit4/
Software tool for estimation of haplotypes aka phasing for SNP array and high coverage sequencing data. The version 4 is refactored and improved version of SHAPEIT algorithm with multiple key additional features.
Proper citation: shapeit4 (RRID:SCR_024335) Copy
https://www.cs.cmu.edu/~ckingsf/software/sailfish/
Software tool that implements novel, alignment free algorithm for estimation of isoform abundances directly from set of reference sequences and RNA-seq reads.
Proper citation: sailfish (RRID:SCR_024326) Copy
https://github.com/fenderglass/Ragout/
Software tool for chromosome level scaffolding using multiple references. Given initial assembly fragments and one or multiple related references it produces chromosome scale assembly.
Proper citation: ragout (RRID:SCR_024206) Copy
https://metacpan.org/dist/Bio-SamTools
Software Perl interface to SamTools library for DNA sequencing.
Proper citation: Bio-SamTools (RRID:SCR_024066) Copy
Software de-novo sequence read assembler for microbial genomes.Designed to create breaks at repeat regions in the genome. This leads to excellent sequence quality without significantly compromising contiguity.SKESA contigs could be connected into GFA graph using GFA connector.
Proper citation: skesa (RRID:SCR_024341) Copy
https://github.com/phac-nml/sistr_cmd
SISTR command-line tool. Open web accessible tool for rapidly typing and subtyping draft salmonella genome assemblies.
Proper citation: sistr (RRID:SCR_024342) Copy
https://metacpan.org/dist/Bio-SCF
Software Perl extension for reading and writting SCF sequence files.This module provides Perl interface to SCF DNA sequencing files. It has both tied hash and an object-oriented interfaces. It provides the ability to read fields from SCF files and limited ability to modify them and write them back.
Proper citation: Bio-SCF (RRID:SCR_024068) Copy
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