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https://pynwb.readthedocs.io/en/latest/

Software Python package for working with Neurodata stored in Neurodata Without Borders files. Software providing API allowing users to read and create NWB formatted HDF5 files. Developed in support to NWB project with aim of spreading standardized data format for cellular based neurophysiology information.

Proper citation: PyNWB (RRID:SCR_017452) Copy   

•   Source: SciCrunch Registry

http://technelysium.com.au/?page_id=13

Software ideal for the most basic of sequencing projects, where assembly of multiple sequences is not required., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Chromas (RRID:SCR_000598) Copy   

•   Source: SciCrunch Registry

http://subread.sourceforge.net/

Software package for high-performance read alignment, quantification and mutation discovery.General purpose read aligner which can be used to map both genomic DNA-seq reads and RNA-seq reads. Subread aligner as fast, accurate and scalable read mapping by seed-and-vote.These programs were also implemented in Bioconductor R package Rsubread.

Proper citation: Subread (RRID:SCR_009803) Copy   

•   Source: SciCrunch Registry

Ratings or validation data are available for this resource

http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/

Software tool to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files for directional, non-directional or paired-end sequencing. Wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for Reduced Representation Bisulfite Sequencing data.

Proper citation: Trim Galore (RRID:SCR_011847) Copy   

•   Source: SciCrunch Registry

https://omictools.com/tiltpicker-tool

Software tool to facilitate particle selection in single particle electron microscopy. An interactive graphical interface application designed to streamline the selection of particle pairs from tilted-pair datasets. Designed to work with existing software tools for image processing.

Proper citation: TiltPicker (RRID:SCR_016674) Copy   

•   Source: SciCrunch Registry

https://github.com/isovic/racon

Software tool as de novo genome assembly from long uncorrected reads. Used to correct raw contigs generated by rapid assembly methods which do not include consensus step. Supports data produced by Pacific Biosciences and Oxford Nanopore Technologies.

Proper citation: Racon (RRID:SCR_017642) Copy   

•   Source: SciCrunch Registry

https://github.com/TransDecoder/TransDecoder

Software tool to identify candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to genome using Tophat and Cufflinks.Starts from FASTA or GFF file. Can scan and retain open reading frames (ORFs) for homology to known proteins by using BlastP or Pfam search and incorporate results into obtained selection. Predictions can then be visualized by using genome browser such as IGV.

Proper citation: TransDecoder (RRID:SCR_017647) Copy   

•   Source: SciCrunch Registry

https://www.sanger.ac.uk/science/tools/reapr

Software tool to identify errors in genome assemblies without need for reference sequence. Can be used in any stage of assembly pipeline to automatically break incorrect scaffolds and flag other errors in assembly for manual inspection. Reports mis-assemblies and other warnings, and produces new broken assembly based on error calls.

Proper citation: Recognition of Errors in Assemblies using Paired Reads (RRID:SCR_017625) Copy   

•   Source: SciCrunch Registry

https://github.com/wdecoster/nanofilt

Software tool written in Python to perform its filtering based on mean read quality and GC content and read length. Used for filtering and trimming of long read sequencing data.

Proper citation: NanoFilt (RRID:SCR_016966) Copy   

•   Source: SciCrunch Registry

https://github.com/mandricigor/ScaffMatch

Software tool as scaffolding algorithm based on maximum weight matching able to produce high quality scaffolds from next generation sequencing data (reads and contigs). Able to handle reads with both short and long insert sizes.

Proper citation: ScaffMatch (RRID:SCR_017025) Copy   

•   Source: SciCrunch Registry

http://rosalind.info/

A software infrastructure, course and tool set for teaching bioinformatics, and biology through the use of models. This platform for learning bioinformatics through problem solving aims to make learning bioinformatics fun and easy. Learning bioinformatics usually requires solving computational problems of varying difficulty that are extracted from real challenges of molecular biology. Rosalind offers an array of intellectually stimulating problems that grow in biological and computational complexity; each problem is checked automatically, so that the only resource required to learn bioinformatics is an internet connection. Rosalind also promises to facilitate improvements in standard bioinformatics education by providing a vital teaching aid and a central homework resource. Rosalind is inspired by Project Euler, Google Code Jam, and the ever growing movement of free online courses. The project''s name commemorates Rosalind Franklin, whose X-ray crystallography with Raymond Gosling facilitated the discovery of the DNA double helix by Watson and Crick. We hope that Rosalind will inspire a new generation of bioinformatics students by attracting biologists who want to develop vital programming skills at their own pace in a unique environment as well as programmers who have never been exposed to some of the stimulating computational problems generated by molecular biology.

Proper citation: Rosalind (RRID:SCR_006233) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/skewer/

Software program for adapter trimming that is specially designed for processing Illumina paired-end sequences.

Proper citation: skewer (RRID:SCR_001151) Copy   

•   Source: SciCrunch Registry

http://www.ccmb.med.umich.edu/ccdu/SNPAAMapper

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2025. A downstream variant annotation program that can effectively classify variants by region (e.g. exon, intron, etc), predict amino acid change type (e.g. synonymous, non-synonymous mutation, etc), and prioritize mutation effects (e.g. CDS versus 5?UTR, etc). Major features: * The pipeline accepts the VCF (Variant Call Format) input file in tab-delimited format and processes the vcf input file containing all cases (G5, lowFreq, and novel) * The variant mapping step has the option of letting users select whether they want to report the bp distance between each identified intron variant and its nearby exon * The pipeline can deal with VCF files called by different SAMTools versions (0.1.18 and older ones) and also offers flexibility in dealing with vcf input files generated using SAMTools with two or three samples * The spreadsheet result file contains full protein sequences for both ref and alt alleles, which makes it easier for downstream protein structure/function analysis tools to take

Proper citation: SNPAAMapper (RRID:SCR_002012) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/apps/mediawiki/mummergpu/index.php?title=MUMmerGPU

Software tool as high throughput DNA sequence alignment program that runs on nVidia G80-class GPUs. Aligns sequences in parallel on video card to accelerate widely used serial CPU program MUMmer.

Proper citation: MUMmerGPU (RRID:SCR_001200) Copy   

•   Source: SciCrunch Registry

http://www.scrm.uzh.ch/biobank.html

The SCRM-CTBB offers state-of-the-art infrastructure and technologies (e.g. cryogenic work bench, semiautomatic cryogenic storage system, uninterrupted cooling chain) and is structured into two areas, including research and a GMP/GCP regulated therapeutic applications. Research: For pre-clinical studies, the SCRM-CTBB provides researchers guidance regarding cell and tissue cryo-preservation, comprising registration, handling, storage and distribution. In order to ensure complete traceability on samples and belonging information all processes are controlled by a Laboratory Information Management System (LIMS) and Quality Assurance (QA) system. The SCRM Biobank is designed to create database that allows connection with other biobanks nationally and internationally. This meta-data file will enable a unique scientific resource for interdisciplinary research. For every new study a contract is established describing the study and the disposition rights. Assistance in writing Biobank Agreements (BAs) and Material Transfer Agreements (MTAs) is provided. Therapeutical applications: As a new feature, apart from research, the SCRM Biobank enables the asservation and preservation of cells and tissues under GMP conditions for later therapeutic use. A special focus will be on a conceptional combination of private and public umbilical cord blood banking (hybrid banking), which allows autologous and/or allogeneic cell applications.

Proper citation: University of Zurich SCRM - Cell-and Tissue Biobank (RRID:SCR_004959) Copy   

•   Source: SciCrunch Registry

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

Software package for the analysis of Ct values from high throughput quantitative real-time PCR (qPCR) assays across multiple conditions or replicates. The input data can be from spatially-defined formats such ABI TaqMan Low Density Arrays or OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad Laboratories; conventional 96- or 384-well plates; or microfluidic devices such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data loading, quality assessment, normalization, visualization and parametric or non-parametric testing for statistical significance in Ct values between features (e.g. genes, microRNAs).

Proper citation: HTqPCR (RRID:SCR_003375) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/NanoStringNorm/

Software package for normalizing, diagnostics and visualization of NanoString nCounter data. Key features include an extensible environment for method comparison and new algorithm development, integrated gene and sample diagnostics, and facilitated downstream statistical analysis.

Proper citation: NanoStringNorm (RRID:SCR_003382) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 12,2024. Updated version of SOAP software for short oligonucleotide alignment that features in super fast and accurate alignment for huge amounts of short reads generated by Illumina/Solexa Genome Analyzer., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: SOAPaligner/soap2 (RRID:SCR_005503) Copy   

•   Source: SciCrunch Registry

http://www.ch.embnet.org/software/COILS_form.html

COILS is a program that compares a sequence to a database of known parallel two-stranded coiled-coils and derives a similarity score. By comparing this score to the distribution of scores in globular and coiled-coil proteins, the program then calculates the probability that the sequence will adopt a coiled-coil conformation.

Proper citation: COILS: Prediction of Coiled Coil Regions in Proteins (RRID:SCR_008440) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.13/bioc/html/epigenomix.html

Software package for the integrative analysis of microarray based gene expression and histone modification data obtained by ChIP-seq. The package provides methods for data preprocessing and matching as well as methods for fitting bayesian mixture models in order to detect genes with differences in both data types.

Proper citation: epigenomix (RRID:SCR_006407) Copy   

•   Source: SciCrunch Registry