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https://github.com/mateidavid/fast5
Software C++ library for accessing Oxford Nanopore Technologies sequencing data.
Proper citation: Fast5 Library (RRID:SCR_024023) Copy
Software provides command line interface and Python API for working with Biological Observation Matrix files.
Proper citation: python-biom-format (RRID:SCR_024193) Copy
https://github.com/Brazelton-Lab/seq-annot
Software Python package for annotating and counting genomic features in genomes and metagenomes. Software tools to facilitate annotation and comparison of genomes and metagenomes.
Proper citation: seq-annot (RRID:SCR_018731) Copy
https://github.com/almorlio/CiLiQuant
Software tool to separate junction reads based on their linear or circular origin. Only non ambiguous junction reads are used to compare relative linear and circular transcript abundance.
Proper citation: CiLiQuant (RRID:SCR_019319) Copy
Open Source software package for digital pathology image analysis. Used for whole slide image analysis and digital pathology. Provides researchers with batch processing and scripting functionality, and extensible platform with which to develop and share new algorithms to analyze complex tissue images.
Proper citation: QuPath (RRID:SCR_018257) Copy
https://sourceforge.net/projects/tab2mage/
Software package written and supported by the ArrayExpress curation team, which aims to ease the process of submitting large microarray experiment datasets.Tab2MAGE uses flexible spreadsheet format for MIAME annotation of microarray experiments.Spreadsheets may be submitted directly to ArrayExpress, or used to generate MAGE-ML for data exchange.
Proper citation: Tab2MAGE (RRID:SCR_024101) Copy
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
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
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
https://github.com/gpertea/gclib
Software genomic C++ library of reusable code for bioinformatics projects.Provides core collection of data structures, trying to avoid unnecessary code dependencies of other heavy libraries, while minimizing build time.
Proper citation: GCLib (RRID:SCR_024028) Copy
https://github.com/RoelofBerg/limereg
Open source commandline based application and/or software development library, that performs 2D, rigid image registration on two greyscale images and outputs either the transformation parameters or the registered image.
Proper citation: limereg (RRID:SCR_024097) Copy
https://neobio.sourceforge.net/
Software library of sequence alignment algorithms implemented in Java.
Proper citation: NeoBio (RRID:SCR_024131) Copy
http://murasaki.dna.bio.keio.ac.jp/wiki/
Software language-theory based homology detection tool across multiple large genomes.
Proper citation: Murasaki (RRID:SCR_024132) Copy
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
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
https://github.com/xdf-modules/libxdf
Software cross-platform C++ library for loading multimodal, multi-rate signals stored in XDF files. Used in biosignal viewing application SigViewer and the LSL application XDFStreamer. Can also be integrated into other C++ applications.
Proper citation: Libxdf (RRID:SCR_024096) Copy
https://github.com/WorkflowConversion/CTDConverter
Software Python scripts to convert CTD files into other formats such as Galaxy, CWL.
Proper citation: CTDConverter (RRID:SCR_024007) Copy
https://github.com/wdecoster/NanoPlot
Software package as plotting tool for long read sequencing data and alignments.
Proper citation: NanoPlot (RRID:SCR_024128) Copy
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
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
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