Lindemann Software

The Lindemann lab actively develops software to aid in the investigation of microbial genetics questions. Our software is always open-source and we encourage scientists to use and build upon our development work.

Lindemann Pipelines

 The Lindemann lab aims to increase scientific reproducibility and data provenance through robust software solutions. Our research heavily relies upon pipelines to reduce analysis times and ensure reproducibility not only across experiments but across scientists.

Software Projects

Software projects both ongoing and being supported by the Lindemann Lab

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Caragols is a configuration library that is coupled with other applications in order to extend reporting, configuration settings, and command line invocation capabilities.

link: caragols

authors: Nathan Denny, Dane Deemer

release: 2023




GeneralTools are general tools we've developed to aid in our day-to-day bioinformatic needs. Instead of creating 1-off scripts and losing them or putting them in personal locations, we created a package that houses our library of scripts and allow anybody to use our tools. Any time we write code we think could be valuable for other causes, we increase the flexibility as needed and add to the library of this package.

link: GeneralTools

authors: Dane Deemer

release: 2022


This is the GENOme anoTATOR (Genotator) package requires an ncbi taxon ID and will pull all genomes from the database, verify, scrub & filter, and annotate them. Pretty cool.

link: GenomeAnnotator

authors: Dane Deemer

release: 2021


This is the Mostly Automated and Rapid Genome Inference Environment that is currently being planned and developed. The purpose of this is to create the most robust annotation pipeline with principals of scalability and data provenance tracking built in.


authors: Dane Deemer, Stephen Lindemann

release: TBD

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This fun package contains tons of SnakeMake pipelines and corresponding utilities and executables. Built around extending the SnakeMake wrapper notion, this is a downloadable package that allows users to harness all the wrappers and pipelines using an executable with only having to specify changes to the config.yaml file in to execute.

link: MetagenomicsPipelines

authors: Dane Deemer

release: 2021


This software aids in the alignment of 2+ genomes to compare synteny, or the arrangement of genes along the chromosome. The output is a simple excel file that is easy to immediately gather insight on or add to other analyses.

link: SyntenyAnalysis

authors: Dane Deemer

release: 2021


Tidy & Organized Analysis of Dna (TOAD) is a command-line tool used to store and query sequencing and biological data in a MongoDB with extreme scalability. It is currently being implemented on Purdue's Geddes cluster using a sharded MongoDB. This software is the gatekeeper to the Data Lake, allowing users to modularly harness top computing resources to store and query organized sequencing data.

link: toad

authors: Nathan Denny, Dane Deemer

release: 2023