Middle-Author-Bioinformatics

Project maintained by Arkadiy-Garber Hosted on GitHub Pages — Theme by mattgraham

Welcome to Middle Author Bioinformatics

Over the past decade, sequencing has become cheap and accessible. However, data analysis is time and labor-intensive. Why get bogged down in the technical details and bioinformatics methods/pipelines that are required for analysis? Because it’s fun? Maybe. But if you don’t have a background in programming and bioinformatics, the learning curve to get any analysis done is steep.

Middle Author Bioinformatics services include consultation, data analysis, custom software and pipeline development, as well as collaboration. Additionally, we offer personalized training workshops that can be lab or department-wide. In addition to programming and bioinformatics, we are trained biologists, with many years of experience in microbiology, microbial ecology, evolutionary biology, and geomicrobiology. All services include a 24/7 direct line of communication - in other words, the analysis will not take a ‘one-size-fits-all’ or ‘plug-and-chug’ approach. Rather, it will be highly customized to the needs of the data and, importantly, the science.

If you are interested, please contact us for a complimentary consultation. We’d would be happy to discuss your data and research questions. This can be a discussion regarding broad questions like the range of analyses that can be done with the data. It can also be more specific.

Services offered

Software Packages

  1. ParaHunter: Identification of gene paralogs within genomes, and calculation of dS and dN/dS values for paralogous gene pairs. Software; Article

  2. Pseudofinder: Identification and analysis of pseudogenes in prokaryotic genomes. Software; Article

  3. FeGenie: HMM-based identification and categorization of iron genes and iron gene operons in genomes and metagenomes. Software; Article

  4. SprayNPray: Rapid and simple taxonomic profiling of genome and metagenome contigs (https://github.com/Arkadiy-Garber/SprayNPray).

  5. MagicLamp: toolkit for annotation of ‘omics datasets using curated HMM sets (https://github.com/Arkadiy-Garber/MagicLamp).

  6. Taxonsluice: Reference-based, heuristic algorithm for identification of potential contaminants in amplicon datasets (https://github.com/Arkadiy-Garber/taxonsluice).

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