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http://colibread.inria.fr/software/mapsembler2/

Targeted assembly software. It takes as input any number of NGS raw read sets and starter set of input sequences.May be used to Validate assembled sequence, Check if known enzyme is present in metagenomic NGS read set, Enrich unmappable reads by extending them, Check what happens at the extremities of a contig, Check the presence / absence and quantify RNA seq splicing events, Check presence/absence of SNPs or structural variants.

Proper citation: Mapsembler2 (RRID:SCR_024102) Copy   

•   Source: SciCrunch Registry

https://github.com/gerddie/maxflow

Software library that implements the maxflow-mincut algorithm.Used for computing mincut/maxflow in a graph.

Proper citation: MAXFLOW (RRID:SCR_024103) Copy   

•   Source: SciCrunch Registry

https://github.com/RabadanLab/arcasHLA

Software tool for high resolution HLA typing from RNAseq. Fast and accurate in silico inference of HLA genotypes from RNA-seq.

Proper citation: arcasHLA (RRID:SCR_022286) Copy   

•   Source: SciCrunch Registry

https://harvest.readthedocs.io/en/latest/content/parsnp.html

Software to align the core genome of hundreds to thousands of bacterial genomes. Input can be both draft assemblies and finished genomes, and output includes variant (SNP) calls, core genome phylogeny and multi-alignments. Parsnp leverages contextual information provided by multi-alignments surrounding SNP sites for filtration/cleaning, in addition to existing tools for recombination detection/filtration and phylogenetic reconstruction.

Proper citation: Parsnp (RRID:SCR_024153) Copy   

•   Source: SciCrunch Registry

https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/apbs/pdb2pqr.html

Software interface for running PDB2PQR web service. Used to prepare structures for further calculations by reconstructing missing atoms, adding hydrogens, assigning atomic charges and radii from specified force fields, and generating PQR files.

Proper citation: PDB2PQR (RRID:SCR_024155) Copy   

•   Source: SciCrunch Registry

https://github.com/sib-swiss/pftools3

Software suite of tools to build and search generalized profiles.

Proper citation: PfTools (RRID:SCR_024158) Copy   

•   Source: SciCrunch Registry

https://jydu.github.io/physamp/

Software package dedicated to phylogenetic sampling. Used to sample sequence alignment according to its corresponding phylogenetic tree.

Proper citation: PhySamp (RRID:SCR_024159) Copy   

•   Source: SciCrunch Registry

https://github.com/GATB/bcalm

Software tool for constructing compacted de Bruijn graph from sequencing data.Parallel algorithm that distributes the input based on minimizer hashing technique, allowing for good balance of memory usage throughout its execution.

Proper citation: BCALM 2 (RRID:SCR_023975) Copy   

•   Source: SciCrunch Registry

https://www.ncbi.nlm.nih.gov/books/NBK179288/

Software provides access to NCBI's suite of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from Unix terminal window. Search terms are entered as command-line arguments. Individual operations are connected with Unix pipes to construct multi-step queries. Selected records can then be retrieved in variety of formats.

Proper citation: Entrez Direct (RRID:SCR_024136) Copy   

•   Source: SciCrunch Registry

https://doua.prabi.fr/software/njplot

Software tool as tree drawing program to draw any phylogenetic tree expressed in Newick phylogenetic tree format (e.g., the format used by the PHYLIP package).Used for rooting the unrooted trees obtained from parsimony, distance or maximum likelihood tree-building methods.

Proper citation: NJplot (RRID:SCR_024137) Copy   

•   Source: SciCrunch Registry

https://www.syngene.com/software/genetools-automatic-image-analysis/

Software package includes comprehensive tools to provide full range of analysis for applications including chemiluminescence, chemifluorescence, fluorescence, colorimetric imaging and colony counting.

Proper citation: GeneTools (RRID:SCR_022505) Copy   

•   Source: SciCrunch Registry

https://github.com/PedroBarbosa/Prepare_SplicingPredictors

Software tool as set of scripts to prepare the input for several sequence-based RNA splicing methods from VCF files.

Proper citation: Prepare_SplicingPredictors (RRID:SCR_023316) Copy   

•   Source: SciCrunch Registry

https://github.com/wdecoster/NanoPlot

Software package as plotting tool for long read sequencing data and alignments.

Proper citation: NanoPlot (RRID:SCR_024128) Copy   

•   Source: SciCrunch Registry

https://pypi.org/project/OBITools/

Software package for analysing NGS data in DNA metabarcoding context. Used to filter and edit sequences while taking into account taxonomic annotation to set up tailor-made analysis pipelines for broad range of DNA metabarcoding applications, including biodiversity surveys or diet analyses.

Proper citation: OBITools (RRID:SCR_024141) Copy   

•   Source: SciCrunch Registry

https://freeimage.sourceforge.io/

Open Source software library for developers who would like to support popular graphics image formats like PNG, BMP, JPEG, TIFF and others as needed by today's multimedia applications.

Proper citation: FreeImage (RRID:SCR_024022) Copy   

•   Source: SciCrunch Registry

https://www.orthanc-server.com/

Open source lightweight DICOM server for medical imaging.Vendor neutral archive to automate and optimize imaging flows. Can be extended with plugins that provide solutions for teleradiology, digital pathology, or enterprise ready databases.

Proper citation: Orthanc (RRID:SCR_024145) Copy   

•   Source: SciCrunch Registry

http://gdcm.sourceforge.net/

GDCM includes file format definition and network communications protocol, both of which should be extended to provide full set of tools for researcher or small medical imaging vendor to interface with existing medical database.Implementation of DICOM standard designed to be open source so that researchers may access clinical data directly.

Proper citation: GDCM (RRID:SCR_024027) Copy   

•   Source: SciCrunch Registry

http://openigtlink.org/

Open source software network communication interface for image guided interventions.Provides plug-and-play unified real-time communications in operating rooms for image-guided interventions, where imagers, sensors, surgical robots,and computers from different vendors work cooperatively to ensure seamless data flow among those components and enable a closed loop process of planning, control, delivery, and feedback.

Proper citation: OpenIGTLink (RRID:SCR_024148) Copy   

•   Source: SciCrunch Registry

https://github.com/brainglobe/bg-atlasapi

Software lightweight python module to interact with atlases for systems neuroscience. Provides consistent way to process brain atlas data from various sources.

Proper citation: BrainGlobe Atlas API (RRID:SCR_023848) Copy   

•   Source: SciCrunch Registry

https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc

Software analysis pipelines that process Chromium Single Cell Multiome ATAC + Gene Expression sequencing data to generate variety of analyses pertaining to gene expression , chromatin accessibility, and their linkage. Used to perform analyses that link chromatin accessibility and GEX.

Proper citation: Cell Ranger ARC (RRID:SCR_023897) Copy   

•   Source: SciCrunch Registry