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http://zhoulab.usc.edu/TopDom/

Software tool to identify Topological Domains, which are basic builiding blocks of genome structure. Detects topological domains in a linear time., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: TopDom (RRID:SCR_016964) Copy   

•   Source: SciCrunch Registry

https://github.com/TGAC/KAT

Software that generates, analyses and compares k-mer spectra produced from sequence files. Used to quality control NGS datasets and genome assemblies.

Proper citation: KAT (RRID:SCR_016741) Copy   

•   Source: SciCrunch Registry

http://maizedig.maizegdb.org/

Genotype and phenotype database for maize images based on BioDIG. Supports multiple reference genomes and has been integrated with the MaizeGDB Genome Browser to make custom tracks showing mutant phenotypes within their genomic context. Allows for custom tagging of images to highlight regions related to the phenotypes. This is accomplished through an interface allowing users to create links from images to genomic coordinates and to curate and search images by gene model ID, gene symbol, and gene name.

Proper citation: Maize Database of Images and Genomes (RRID:SCR_016987) Copy   

•   Source: SciCrunch Registry

https://rvista.dcode.org/

Web tool for analyzing regulatory potential of noncoding sequences. rVISTA web server is interconnected with TRANSFAC database, allowing users to either search for matrices present in TRANSFAC library collection or search for user defined consensus sequences. rVISTA 2.0 web server is used for high throughput discovery of cis-regulatory elements. Can process alignments generated by zPicture and blastz alignment programs or use pre-computed pairwise alignments of several vertebrate genomes available from ECR Browser and GALA database. Evolutionary analysis of transcription factor binding sites.

Proper citation: rVista (RRID:SCR_018707) Copy   

•   Source: SciCrunch Registry

http://funcoup.sbc.su.se/search/

Database of genome wide functional coupling networks. Provides tools to explore predicted networks and to retrieve detailed information about data underlying each prediction. Web service for functional coupling search.

Proper citation: FunCoup (RRID:SCR_018711) Copy   

•   Source: SciCrunch Registry

http://smithlabresearch.org/software/preseq/

Software package for predicting library complexity and genome coverage in high throughput sequencing. Aimed at predicting yield of distinct reads from genomic library from initial sequencing experiment. Predicting molecular complexity of sequencing libraries.

Proper citation: Preseq (RRID:SCR_018664) Copy   

•   Source: SciCrunch Registry

https://www.otago.ac.nz/chatterjee-lab/tools/index.html

Software package for large scale genomic DNA methylation analysis. Filters and processes aligned bisulphite sequenced data to generate comprehensive reference methylomes in different units for any genome. Processes aligned SAM files of multiple samples to provide reliable and statistically significant differentially methylated regions, then relate them to proximal genes and CpG features with reasonable rapidity.

Proper citation: Differential Methylation Analysis Package (RRID:SCR_019148) Copy   

•   Source: SciCrunch Registry

http://enterobase.warwick.ac.uk/

Integrated software environment that supports identification of global population structures within several bacterial genera that include pathogens. Web service for analyzing and visualizing genomic variation within bacteria. Genome database to enable to identify, analyse, quantify and visualise genomic variation within bacterial genera including Salmonella, Escherichia/Shigella, Clostridioides,Vibrio,Yersinia,Helicobacter,Moraxella.

Proper citation: EnteroBase (RRID:SCR_019019) Copy   

•   Source: SciCrunch Registry

https://github.com/Rinoahu/SwiftOrtho

Software tool for orthology analysis to identify orthologs, paralogs and co orthologs for genomes. Used to perform homology classification across genomes of different species in large genomic datasets.

Proper citation: SwiftOrtho (RRID:SCR_017122) Copy   

•   Source: SciCrunch Registry

https://github.com/fenderglass/Flye

Software package as de novo assembler for single molecule sequencing reads. Used for assembling long, error prone reads such as those produced by PacBio and Oxford Nanopore Technologies, for fast and accurate genome reconstructions. Available for Linux and MacOS platforms.

Proper citation: Flye (RRID:SCR_017016) Copy   

•   Source: SciCrunch Registry

https://github.com/im3sanger/dndscv

Software R package as suite of dN/dS methods to quantify selection in cancer and somatic evolution. Contains functions to quantify dN/dS ratios for missense, nonsense and essential splice mutations, at level of individual genes, groups of genes or at whole genome level. Used to detect cancer driver genes on datasets.

Proper citation: dndSCV (RRID:SCR_017093) Copy   

•   Source: SciCrunch Registry

https://github.com/josephryan/matemaker

Software tool to make artificial mate pairs from long sequences for scaffolding.

Proper citation: matemaker (RRID:SCR_017199) Copy   

•   Source: SciCrunch Registry

http://www.cbs.dtu.dk/services/RNAmmer/

Software package to predict ribosomal RNA genes in full genome sequences by utilising two levels of Hidden Markov Models. Consistent and rapid annotation of ribosomal RNA genes.

Proper citation: RNAmmer (RRID:SCR_017075) Copy   

•   Source: SciCrunch Registry

https://github.com/BDI-pathogens/phyloscanner

Software tool for analysing pathogen genetic diversity and relationships between and within hosts at once, in windows along genome. Inferring transmission from within and between host pathogen genetic diversity.

Proper citation: phyloscanner (RRID:SCR_017400) Copy   

•   Source: SciCrunch Registry

https://github.com/ruanjue/wtdbg2.git

Software tool as de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies. It assembles raw reads without error correction and then builds consensus from intermediate assembly output. Desiged to assemble huge genomes in very limited time.

Proper citation: WTDBG (RRID:SCR_017225) Copy   

•   Source: SciCrunch Registry

https://github.com/theaidenlab/3d-dna.git

Software tool as 3D de novo assembly (3D DNA) pipeline. Used to help generate HI-C assembly.

Proper citation: 3D de novo assembly (RRID:SCR_017227) Copy   

•   Source: SciCrunch Registry

https://www.drive5.com/piler/

Software tool for analyzing repetitive DNA found in genome sequences. Software package for identification and classification of genomic repeats. Used for identifying patterns of local alignments induced by certain classes of repeats.

Proper citation: PILER (RRID:SCR_017333) Copy   

•   Source: SciCrunch Registry

https://github.com/tanghaibao/mcscan

Software package to simultaneously scan multiple genomes to identify homologous chromosomal regions and subsequently align these regions using genes as anchors.Used to identify conserved gene arrays both within same genome and across different genomes. Command line program to wrap dagchainer and combine pairwise results into multi alignments in column format.

Proper citation: MCScan (RRID:SCR_017650) Copy   

•   Source: SciCrunch Registry

https://blobtools.readme.io/docs

Software tool as modular command line solution for visualisation, quality control and taxonomic partitioning of genome datasets. Used for interrogation of genome assemblies. Assists in primary partitioning of data, leading to improved assemblies, and screening of final assemblies for potential contaminants.

Proper citation: Blobtools (RRID:SCR_017618) Copy   

•   Source: SciCrunch Registry

https://github.com/philres/ngmlr

Software tool as long read mapper designed to align PacBio or Oxford Nanopore reads to reference genome and optimized for structural variation detection.

Proper citation: Ngmlr (RRID:SCR_017620) Copy   

•   Source: SciCrunch Registry