- perl
- linux
- workflows
- pipelines
- productivity
- snakemake
- python
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- nanopore
- illumina
- QC
- assembly
- comparative genomics
- phylogenomics
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Illumina vs. Nanopore for Plant Pathogens — A Practical Overview
A practical, lab-oriented comparison of Illumina and Nanopore sequencing for plant pathogens, grounded in real Snakemake workflows.
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Two New Snakemake Pipelines for Bacteriophage Assembly and QC: Illumina and Nanopore
Two new Snakemake pipelines for bacteriophage genome assembly and quality control: one for Illumina reads and one for Nanopore reads.
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Rapid and Reproducible RSSC Sequevar Typing with Snakemake
A Snakemake pipeline for automated Ralstonia solanacearum species complex (RSSC) sequevar typing based on the endoglucanase (egl) gene — from genome assemblies to phylogenetic tree and sequevar assignment in one command.
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Superior Bacterial Genome Assembly with Autocycler Consensus and Snakemake
A comprehensive Snakemake pipeline that leverages Autocycler consensus assembly to achieve superior quality bacterial genomes from Oxford Nanopore sequencing data
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Adventures in Bacterial Genome Assembly with Snakemake
A tour of my Snakemake pipelines for bacterial genome assembly and QC, inspired by the work of Dr. Ryan Wick and Dr. Torsten Seeman.