Tools   Select Another Resource Report Type

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

http://refgenie.databio.org

Software tool to organize, retrieve, and share genome analysis resources. Reference genome assembly asset manager. In addition to genome indexes, can manage any files related to reference genomes, including sequences and annotation files. Includes command line interface and server application that provides RESTful API, so it is useful for both tool development and analysis.

Proper citation: refgenie (RRID:SCR_017574) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/TCGAbiolinks/

Software R Bioconductor package for integrative analysis with TCGA data.TCGAbiolinks is able to access National Cancer Institute Genomic Data Commons thorough its GDC Application Programming Interface to search, download and prepare relevant data for analysis in R.

Proper citation: TCGAbiolinks (RRID:SCR_017683) Copy   

•   Source: SciCrunch Registry

https://crispy.secondarymetabolites.org

Web tool to design sgRNAs for CRISPR applications. Web tool based on CRISPy to design sgRNAs for any user-provided microbial genome. Implemented as standalone web application for Cas9 target prediction.

Proper citation: CRISPy-web (RRID:SCR_017970) Copy   

•   Source: SciCrunch Registry

https://github.com/slimsuite/pafscaff

Software as Pairwise mApping Format reference based Scaffold anchoring and super scaffolding tool. Dsigned for mapping genome assembly scaffolds to closely related chromosome level reference genome assembly.

Proper citation: PAFScaff (RRID:SCR_017976) Copy   

•   Source: SciCrunch Registry

https://github.com/santeripuranen/SpydrPick

Software command line tool for performing direct coupling analysis of aligned categorical datasets. Used for analysis at scale of pan genomes of many bacteria. Incorporates correction for population structure, which adjusts for phylogenetic signal in data without requiring explicit phylogenetic tree.

Proper citation: SpydrPick (RRID:SCR_018176) Copy   

•   Source: SciCrunch Registry

https://github.com/santeripuranen/SuperDCA

Software tool for global direct coupling analysis of input genome alignments. Implements variant of pseudolikelihood maximization direct coupling analysis, with emphasis on optimizations that enable its use on genome scale. May be used to discover co evolving pairs of loci.Used for genome wide epistasis analysis.

Proper citation: SuperDCA (RRID:SCR_018175) Copy   

•   Source: SciCrunch Registry

https://metacpan.org/pod/Bio::CUA

Software tool as flexible and comprehensive codon usage analyzer. Used to analyze codon usage bias (CUB) and relevant problems.

Proper citation: Codon Usage Analyzer (RRID:SCR_018500) 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://cm.jefferson.edu/rna22/

Software tool as a pattern based algorithm for detecting microRNA binding sites and their corresponding microRNA and mRNA complexes. Allows interactive exploration and visualization of miRNA target predictions. Permits link-out to external expression repositories and databases.

Proper citation: RNA22 (RRID:SCR_016507) Copy   

•   Source: SciCrunch Registry

https://pan.genomics.cn/ucdisk/s/VjuIRb&code=877833

Pipeline for construction and graphical visualization of annotated pangenome networks from microbial genomes. With the ability to extract and visualize gene contents and gene-gene physical adjacencies of a specific taxon from large-scale metagenomic data provides pangenome analysis to uncultured microbial taxa., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: MetaPGN (RRID:SCR_016472) Copy   

•   Source: SciCrunch Registry

https://www.thermofisher.com/order/catalog/product/00-0210

Scanner for microarray analysis to scan next-generation higher-density arrays, including SNP arrays, tiling arrays for transcription and all-exon arrays for whole-genome analysis.

Proper citation: Thermo Fisher: GeneChip� Scanner 3000 7G (RRID:SCR_016522) Copy   

•   Source: SciCrunch Registry

https://www.ncbi.nlm.nih.gov/biocollections

Registry of bio-collections linked to genomes. Collection of curated dataset of metadata for culture collections, museums, herbaria and other natural history collections, including Darwin Core institution and collection codes, and URL formulae for mapping specimen ids to web pages at the collection site.

Proper citation: NCBI Biocollections (RRID:SCR_016459) Copy   

•   Source: SciCrunch Registry

https://github.com/WGS-TB/MentaLiST

Software for a MLST (multi-locus sequence typing) caller, based on a k-mer counting algorithm and written in the Julia language. Designed and implemented to handle large typing schemes.

Proper citation: MentaLiST (RRID:SCR_016469) Copy   

•   Source: SciCrunch Registry

https://github.com/lh3/fermi

Software assembler and analysis tool for whole-genome short-gun sequencing for Illumina reads. Provides tools for error correction, sequence-to-read alignment and comparison between read sets. Used for large genomes.

Proper citation: fermi (RRID:SCR_016652) Copy   

•   Source: SciCrunch Registry

http://ecogenomics.github.io/CheckM/

Software tool to assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes by using a broader set of marker genes specific to the position of a genome within a reference genome tree and information about the collocation of these genes.

Proper citation: CheckM (RRID:SCR_016646) Copy   

•   Source: SciCrunch Registry