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https://github.com/humanlongevity/HLA

Software tool for fast and accurate HLA typing from short read sequence data. Iteratively refines mapping results at amino acid level to achieve four digit typing accuracy for both class I and II HLA genes, taking only 3 min to process 30× whole genome BAM file on desktop computer.

Proper citation: xHLA (RRID:SCR_022277) Copy   

•   Source: SciCrunch Registry

https://www.gnu.org/software/sed/

Software tool as non interactive command line text editor. Command line that works with streams of characters for searching, filtering and text processing. Used for extracting part of file using pattern matching or substituting multiple occurrences of string within file.

Proper citation: GNU sed (RRID:SCR_018215) Copy   

•   Source: SciCrunch Registry

https://www.gnu.org/software/grep/manual/grep.html

Software tool to searches one or more input files for lines containing a match to a specified pattern. Prints lines that contain match for one or more patterns. Command-line utility for searching plain-text data sets for lines that match regular expression. When finds match, it copies line to standard output (by default), or produces whatever other sort of output you have requested with options.

Proper citation: GNU Grep (RRID:SCR_018212) Copy   

•   Source: SciCrunch Registry

https://github.com/a-h-b/dadasnake

Software tool as snakemake implementation of DADA2 to process amplicon sequencing data for microbial ecology.

Proper citation: dadasnake (RRID:SCR_019149) Copy   

•   Source: SciCrunch Registry

https://www.gnu.org/software/tar/

Software tool to create tar archives, as well as various other kinds of manipulation. Used to extract files, to store additional files, or to update or list files which were already stored. Can direct its output to available devices, files, or other programs, can access remote devices or files.

Proper citation: GNU Tar (RRID:SCR_018216) Copy   

•   Source: SciCrunch Registry

https://www.gnu.org/software/gawk/manual/gawk.html

Software tool to select particular records in file and perform operations upon them. awk utility interprets special purpose programming language that makes it possible to handle simple data reformatting jobs with few lines of code. Source code for latest release of GNU awk is available from GNU project ftp server and its many mirrors.

Proper citation: GNU Awk (RRID:SCR_018211) Copy   

•   Source: SciCrunch Registry

https://github.com/Kingsford-Group/kourami

Software graph guided assembly for novel human leukocyte antigen allele discovery. Graph guided assembly for HLA haplotypes covering typing exons using high coverage whole genome sequencing data.Implemented in Java and supported on Linux and Mac OS X.

Proper citation: Kourami (RRID:SCR_022280) Copy   

•   Source: SciCrunch Registry

https://github.com/almorlio/CiLiQuant

Software tool to separate junction reads based on their linear or circular origin. Only non ambiguous junction reads are used to compare relative linear and circular transcript abundance.

Proper citation: CiLiQuant (RRID:SCR_019319) Copy   

•   Source: SciCrunch Registry

https://github.com/mourisl/Rascaf

Software tool for scaffolding with RNA-seq read alignments. Used for improving genome assembly with RNA sequencing data.

Proper citation: Rascaf (RRID:SCR_022014) Copy   

•   Source: SciCrunch Registry

http://tools.thermofisher.com/content/sfs/manuals/cms_040970.pdf

Automated PCR instrument for automated amplification of nucleic acids with Polymerase Chain Reaction. It has reaction volumes of up to 50 uL and sample temperature range of 4 to 99.9 C.

Proper citation: Thermo Fisher: Applied Biosystems: GeneAmp 9700 PCR Thermocycler System (RRID:SCR_018436) Copy   

•   Source: SciCrunch Registry

https://covidcg.org/?tab=home

Open browser to inform therapeutics development for tracking SARS-CoV-2 single nucleotide variations, lineages, and clades using virus genomes on GISAID database while filtering by location, date, gene, and mutation of interest. can Provides information on which virus mutations are present in area during specific period by processing data on mutations found in viral genetic material collected worldwide from hundreds of thousands of people with COVID-19, which are hosted in existing online database.

Proper citation: COVID CG (RRID:SCR_022266) Copy   

•   Source: SciCrunch Registry

https://github.com/wtsi-hpag/PretextMap

Software tool to convert SAM formatted read pairs into genome contact maps. Prepares alignments for visualization with PretextView.

Proper citation: PretextMap (RRID:SCR_022023) Copy   

•   Source: SciCrunch Registry

https://gitlab.com/PlantGenomicsLab/gFACs

Software package provides comprehensive framework for evaluating, filtering, and analyzing gene models from range of input applications and preparing these annotations for formal publication or downstream analysis.

Proper citation: gFACs (RRID:SCR_022017) Copy   

•   Source: SciCrunch Registry

https://openwetware.org/wiki/HughesLab:JTK_Cycle

Software R package for Detecting Rhythmic Components in Genome-Scale Data Sets. Non-parametric algorithm to identify rhythmic components in large datasets. Identifies and characterizes cycling variables in large datasets.

Proper citation: JTK_CYCLE (RRID:SCR_017962) Copy   

•   Source: SciCrunch Registry

https://openrefine.org/

Open source software Java tool for working with data. Used for loading data, cleaning up data, transforming data from one format into another and extending it with web services and external data.

Proper citation: OpenRefine (RRID:SCR_021305) Copy   

•   Source: SciCrunch Registry

https://github.com/taborlab/FlowCal

Open source software tool for automatically converting flow cytometry data from arbitrary to calibrated units. Can be run using intuitive Microsoft Excel interface, or customizable Python scripts. Software accepts Flow Cytometry Standard (FCS) files as inputs and is compatible with different calibration particles, fluorescent probes, and cell types. Automatically gates data, calculates common statistics, and produces plots.

Proper citation: FlowCal (RRID:SCR_018140) Copy   

•   Source: SciCrunch Registry

https://rubygems.org/gems/viral_seq

Ruby Gem with bioinformatics tools for processing viral NGS data. Specifically for Primer-ID sequencing and HIV drug resistance analysis.

Proper citation: viral_seq (RRID:SCR_018515) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/arts/

Software tool as automated biomarker that outputs score linked to likelihood person sufferring from arteriolosclerosis based on brain MRI data and basic demographic information. MRI data processing pipeline and classifier are packaged into software container.Users do not need to perform any image processing, and are only required to install Singularity to run ARTS.

Proper citation: ARTS biomarker (RRID:SCR_019288) Copy   

•   Source: SciCrunch Registry

https://github.com/berenslab/EphysExtraction

Software tool as code to extract electrophysiological parameters of neurons. Code is continuously being updated to handle more kinds of voltage traces and extract different kinds of features.

Proper citation: EphysExtraction (RRID:SCR_018193) Copy   

•   Source: SciCrunch Registry

https://ibest.github.io/HTStream/

Software tool as quality control and processing pipeline for High Throughput Sequencing data. Uses tab delimited fastq format that allows for streaming from application to application. Interoperable with other standard Linux tools., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: HTStream (RRID:SCR_018354) Copy   

•   Source: SciCrunch Registry