Tools   Select Another Resource Report Type

https://github.com/PacificBiosciences/FALCON

Software package for aligning long sequencing reads as a diploid-aware genome assembler. Used for assembling non-inbred or rearranged heterozygous genomes.

Proper citation: Falcon (RRID:SCR_016089) Copy   

•   Source: SciCrunch Registry

http://www.omicsbean.cn

Software tool for multi-omics data analysis that can perform complex and personalized analysis. Network regulation and molecular mechanism models can be customized according to the requirements of the users.

Proper citation: OmicsBean (RRID:SCR_016322) Copy   

•   Source: SciCrunch Registry

http://zzlab.net/blink/index.html

Software for next level of genome wide association studies with both individuals and markers in millions. The method releases the requirement that causative genes are evenly distributed on genome and consequently boosts statistical power.

Proper citation: BLINK (RRID:SCR_016288) Copy   

•   Source: SciCrunch Registry

https://github.com/Sung-Huan/ANNOgesic

Software tool for bacterial/archaeal RNA-Seq based genome annotations. Used for integrating, detecting, predicting, and grouping RNA-Seq data.

Proper citation: ANNOgesic (RRID:SCR_016326) Copy   

•   Source: SciCrunch Registry

https://omabrowser.org/oma/

Web based database interface for orthology prediction for the inference of orthologs among complete genomes. Used to relate genes across many species., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: OMA Orthology database (RRID:SCR_016425) Copy   

•   Source: SciCrunch Registry

https://github.com/MRCIEU/PhenoSpD

Software toolkit for phenotypic correlation estimation and multiple testing correction (Spectral Decomposition, SpD) for human phenome using genome-wide association study (GWAS) summary statistics. It is a command line R based tool.

Proper citation: PhenoSpD (RRID:SCR_016359) 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://triage.niaid.nih.gov

Platform to facilitate prediction, analysis, and hypothesis generation from genome wide perturbation studies like those designed with RNAi and CRISPR technologies.

Proper citation: TRIAGE (RRID:SCR_016609) 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

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

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

http://sourceforge.net/projects/bbmap

Software tool as a short read aligner for DNA and RNA seq data. Used for large genomes with millions of scaffolds. Can align reads from Illumina, PacBio, 454, Sanger, Ion Torrent, Nanopore. Fast and accurate, particularly with highly mutated genomes or reads with long indels, even whole gene deletions over 100kbp long. It has no upper limit to genome size or number of contigs. Written in Java, can run on any platform.

Proper citation: BBmap (RRID:SCR_016965) Copy   

•   Source: SciCrunch Registry

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

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