Software — Jeff Bailey Lab

We develop software to answer biologic questions and are committed to open source development that can be used in resource limited settings.

MIPTools

A suite of computational tools used for molecular inversion probe design, data processing, and analysis.

Languages/Systems: Singularity container containing, Jupyter Notebooks, Python, Command Line Interface (CLI)

see the website

Software for:
Molecular Inversion Probe Analysis

We develop software to answer biologic questions and are committed to open source development that can be used in resource limited settings.

MIPTools

A suite of computational tools used for molecular inversion probe design, data processing, and analysis.

Languages/Systems: Singularity container containing, Jupyter Notebooks, Python, Command Line Interface (CLI)

see the website

Software for:
Molecular Inversion Probe Analysis

miplicorn

MIPs + amplicons in R. A alpha toolset underdevelopment for common basic analyses on defined-end targeted sequencing (e.g molecular inversion probe and amplicons) . Aims to provides the post microhaplotype to parse, manipulate, analyze, and visualize data—and move formatted data to other more complex analyses.

Languages/Systems: R

see the website

MIPWrangler

Software for rapid analysis of molecular inversion probes in numerous samples. Leveraging core code from SeekDeep it deals with unique molecular identifiers specific to MIPs for Illumina Sequence

Languages: C++

see the webiste

SeekDeep

Single-nucleotide resolution microhaplotype resolution of amplicons. Flexible optimization and additional methods allow for short and long reads as well as multiple sequence inputs including IonTorrent, PacBio, and Illumina with ONT coming soon.

Languages/Systems: C++

See the website