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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/nanoporetech/qcat
Software Python command-line tool for demultiplexing Oxford Nanopore reads from FASTQ files.
Proper citation: qcat (RRID:SCR_024195) Copy
https://github.com/gem-pasteur/macsyfinder
Software tool to mine genomes for molecular systems with Application to CRISPR-Cas Systems. Detection of macromolecular systems in protein datasets using systems modelling and similarity search.
Proper citation: MacSyFinder (RRID:SCR_024106) Copy
https://github.com/SciLifeLab/TIDDIT
Software tool as structural variant calling.
Proper citation: tiddit (RRID:SCR_024361) Copy
https://github.com/Adamtaranto/Yanagiba
Software tool to filter and slice Nanopore reads which have been basecalled with Albacore.
Proper citation: Yanagiba (RRID:SCR_024362) Copy
https://github.com/mateidavid/nanocall
Software basecaller for Oxford Nanopore Technologies sequencing data. Oxford Nanopore Basecaller.
Proper citation: Nanocall (RRID:SCR_024124) Copy
https://github.com/torognes/swarm
Software tool as clustering method for amplicon-based studies.
Proper citation: swarm (RRID:SCR_024358) Copy
https://www.integromics.com/omicsoffice-for-ngs/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. Software for secondary and tertiary analysis of Next Generation Sequencing (NGS) data.
Proper citation: OmicsOffice for NGS SeqSolve (RRID:SCR_001222) Copy
http://www.bioinfor.com/zoom/general/overview.html
Software to map the Illumina/Solexa reads of 15x coverage of a human genome to the reference human genome in one CPU-day, allowing two mismatches, at full sensitivity.
Proper citation: ZOOM (RRID:SCR_002175) 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
https://github.com/Pithikos/C-Thread-Pool
Software for minimal but powerful thread pool in ANSI C.
Proper citation: C Thread Pool (RRID:SCR_023999) Copy
https://github.com/smirarab/sepp/
Ensemble of HMM methods.Repository includes code for SEPP, TIPP, UPP, HIPPI. Methods use ensembles of Hidden Markov Models in different ways, each focusing on different problem.
Proper citation: sepp (RRID:SCR_024327) Copy
https://www.teuniz.net/edflib/
Software programming library for C/C++ to read/write EDF+/BDF+ files.It also reads old-type EDF/BDF files.
Proper citation: EDFlib (RRID:SCR_024010) Copy
http://www.dclunie.com/dicom3tools.html
Software package provides DICOM medical image files manipulation and conversion tools. Command line utilities for creating, modifying, dumping and validating DICOM files.
Proper citation: Dicom3tools (RRID:SCR_024008) Copy
https://github.com/stamatak/AxPcoords.dist
Software tool for large scale co-phylogenetic analyses on several thousands of taxa. Faster than DistPCoA and numerically stable on large datasets.
Proper citation: AxPcoords (RRID:SCR_023971) Copy
http://sco.h-its.org/exelixis/web/software/AxParafit/index.html
Software tool for large scale co-phylogenetic analyses on several thousands of taxa. Allows for rapid and much more thorough computation and analyses of large co-phylogenetic datasets.
Proper citation: AxParafit (RRID:SCR_023968) Copy
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
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