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http://sak042.github.io/Wessim/
Software simulator for a targeted resequencing generally known as exome sequencing. Wessim generates a set of artificial DNA fragments for next generation sequencing (NGS) read simulation.
Proper citation: Wessim (RRID:SCR_002567) Copy
https://github.com/BlaisProteomics/mzStudio
Software tool for proteomics data analysis, visualization, and notebook application. Dynamic digital canvas for user driven interrogation of mass spectrometry data. Operating system Unix/Linux, Windows.
Proper citation: mzStudio (RRID:SCR_017088) Copy
https://github.com/katholt/srst2
Software that is designed to take Illumina sequence data, a MLST database and/or a database of gene sequences (e.g. resistance genes, virulence genes, etc) and report the presence of STs and/or reference genes.
Proper citation: Short Read Sequence Typing for Bacterial Pathogens (RRID:SCR_015870) Copy
https://github.com/INTABiotechMJ/MITE-Tracker
Open source software tool for identifying miniature inverted repeat transposable elements in large genomes. Used to process large scale genomes, to find and classify MITEs using an efficient alignment strategy to retrieve nearby inverted repeat sequences.
Proper citation: MITE-Tracker (RRID:SCR_017030) Copy
https://github.com/Rinoahu/SwiftOrtho
Software tool for orthology analysis to identify orthologs, paralogs and co orthologs for genomes. Used to perform homology classification across genomes of different species in large genomic datasets.
Proper citation: SwiftOrtho (RRID:SCR_017122) Copy
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
https://github.com/common-workflow-language/cwltool
Reference implementation of the Common Workflow Language standards. It provides complete features and tools and comprehensive validation of CWL. The reference implementation consists of two packages. The cwltool package is the primary Python module containing the reference implementation in the cwltool module and console executable by the same name. The cwlref-runner package is optional and provides an additional entry point under the alias cwl-runner, which is the implementation-agnostic name for the default CWL interpreter installed on a host.
Proper citation: cwltool (RRID:SCR_015528) Copy
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