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

Software and server that performs intelligent design of oligonucleotides for DNA microarrays.

Proper citation: OligoWiz (RRID:SCR_012966) Copy   

•   Source: SciCrunch Registry

http://c1.accurascience.com/miRecords/

A resource for animal miRNA-target interactions consisting of the Validated Targets component, a large, high-quality database of experimentally validated miRNA targets resulting from meticulous literature curation, and the Predicted Targets component, an integration of predicted miRNA targets produced by 11 established miRNA target prediction programs. April 27, 2013, the Validated Targets component of miRecords hosts 2705 records of interactions between 644 miRNAs and 1901 target genes in 9 animal species. Among these records, 2028 were curated from low throughput experiments. The Predicted Targets component of mIRecords integrates the predicted targets of the following miRNA target prediction tools: DIANA-microT, MicroInspector, miRanda, MirTarget2, miTarget, NBmiRTar, PicTar, PITA, RNA22, RNAhybrid, and TargetScan/TargertScanS. We would be glad to include your experimentally validated miRNA target data (published or unpublished) into miRecords., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: miRecords (RRID:SCR_013021) Copy   

•   Source: SciCrunch Registry

https://github.com/broadinstitute/pilon/

Software tool to automatically improve draft assemblies and find variation among strains, including large event detection. FASTA files of genome along with one or more BAM files of reads aligned as input. Read alignment analysis is used to identify inconsistencies between input genome and evidence in reads, then attempts to make improvements to genome.

Proper citation: Pilon (RRID:SCR_014731) Copy   

•   Source: SciCrunch Registry

https://ccb.jhu.edu/software/stringtie/

Software application for assembling of RNA-Seq alignments into potential transcripts. It enables improved reconstruction of a transcriptome from RNA-seq reads. This transcript assembling and quantification program is implemented in C++ .

Proper citation: StringTie (RRID:SCR_016323) Copy   

•   Source: SciCrunch Registry

https://github.com/OpenGene/fastp

Software tool to provide fast all in one preprocessing for FastQ files. Developed in C++ with multithreading supported to afford high performance. Performs quality control, adapter trimming, quality filtering, per read quality pruning and many other operations with a single scan of the FASTQ data.

Proper citation: fastp (RRID:SCR_016962) Copy   

•   Source: SciCrunch Registry

https://github.com/HingeAssembler/HINGE

Software application for long read genome assembly based on hinging. Used in long-read sequencing technologies in genome assemblies to achieve optimal repeat resolution.

Proper citation: Hinge (RRID:SCR_016135) Copy   

•   Source: SciCrunch Registry

https://www.rdocumentation.org/packages/pheatmap/versions/0.2/topics/pheatmap

Software tool as a function in R to draw clustered heatmaps for better control over graphical parameters.

Proper citation: pheatmap (RRID:SCR_016418) Copy   

•   Source: SciCrunch Registry

https://github.com/brentp/duphold

Software tool to annotate structural variant calls with sequence depth information that can add or remove confidence to SV predicted to affect copy number. Indicates the presence of a rapid change in depth relative to the regions surrounding the breakpoints. Allows the run time to be nearly independent of the number of variants important for large, jointly called projects with many samples. Annotates structural variant predictions made from both short read and long read data.

Proper citation: duphold (RRID:SCR_016938) Copy   

•   Source: SciCrunch Registry

https://rostlab.org/node/960

Alignment software for large-scale protein contact or protein-protein interaction prediction optimized for speed through shorter runtimes. FreeContact provides the opportunity to compute contact predictions in any environment (desktop or cloud).

Proper citation: FreeContact (RRID:SCR_016113) Copy   

•   Source: SciCrunch Registry

https://github.com/xavierdidelot/clonalorigin

Software package for comparative analysis of the sequences of a sample of bacterial genomes in order to reconstruct the recombination events that have taken place in their ancestry.

Proper citation: ClonalOrigin (RRID:SCR_016061) Copy   

•   Source: SciCrunch Registry

https://sanger-pathogens.github.io/Roary/

Software tool for rapid large scale prokaryote pan genome analysis. Builds large scale pan genomes, identifying core and accessory genes. Makes construction of pan genome of thousands of prokaryote samples on standard desktop without compromising on accuracy of results. Not intended for meta genomics or for comparing extremely diverse sets of genomes.

Proper citation: Roary (RRID:SCR_018172) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/iontree.html

Software package that provides utility functions to manage and analyse MS2/MS3 fragmentation data from ion trap mass spectrometry. It was designed for high throughput metabolomics data with many biological samples and a large numer of ion trees collected. Tests have been done with data from low-resolution mass spectrometry but could be readily extended to precursor ion based fragmentation data from high resoultion mass spectrometry.

Proper citation: iontree (RRID:SCR_002813) Copy   

•   Source: SciCrunch Registry

http://www.sph.umich.edu/csg/qin/HPeak/Readme.html

A Hidden Markov Model-based algorithm for the purpose of defining genome-wide ChIP-enriched peaks in the human genome using short sequence reads.

Proper citation: HPeak (RRID:SCR_010859) Copy   

•   Source: SciCrunch Registry

http://johnsonlab.ucsf.edu/mochi.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2022. Java software that integrates browsing of genomic sequences, features, and data with DNA motif visualization and analysis.

Proper citation: MochiView (RRID:SCR_000259) Copy   

•   Source: SciCrunch Registry

http://soap.genomics.org.cn/soapsplice.html

A tool for genome-wide ab initio detection of splice junction sites from RNA-Seq, a method using new generation sequencing technologies to sequence the messenger RNA.

Proper citation: SOAPsplice (RRID:SCR_013253) Copy   

•   Source: SciCrunch Registry

http://mummer.sourceforge.net/

Software package as system for rapidly aligning entire genomes. Alignment tool for DNA and protein sequences. Can align incomplete genomes.

Proper citation: MUMmer (RRID:SCR_018171) Copy   

•   Source: SciCrunch Registry

http://www.apha.org/

The oldest and most diverse organization of public health professionals in the world and has been working to improve public health since 1872.

Proper citation: APHA (RRID:SCR_012000) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/annotation/argo/

A tool for visualizing and manually annotating whole genomes that can be run as Applet or Webstart application as well as standalone application.

Proper citation: Argo Genome Browser (RRID:SCR_011763) Copy   

•   Source: SciCrunch Registry

http://www.usadellab.org/cms/index.php?page=trimmomatic

Software Java pipeline for trimming tasks for Illumina paired end and single ended data. Flexible Trimmer for Illumina Sequence Data. Pair aware preprocessing tool optimized for Illumina next generation sequencing data. Includes several processing steps for read trimming and filtering. Operating systems Unix/Linux, Mac OS, Windows.

Proper citation: Trimmomatic (RRID:SCR_011848) Copy   

•   Source: SciCrunch Registry

https://github.com/bids-standard/bids-validator

Software validation tool that checks submitted folder structure for compliance to BIDS data standard. Validates Brain Imaging Data Structure.

Proper citation: BIDS Validator (RRID:SCR_017255) Copy   

•   Source: SciCrunch Registry