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Elizabeth A. McDaniel
Scientist
Scientist interested in microbial communities, metagenomics, & reproducible computing
SC
TR
Published: Feb 21, 2023
seqqc is a Nextflow pipeline for quality control of short- or long-read sequencing data. It quickly assesses the quality of sequencing data so that it can be posted to a public repository before analysis for biological insights. Faster open data, faster knowledge for everyone.
Connections
SC
RD
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+1
Published: Feb 21, 2023
The sourmash Python package produces many outputs that describe the content and similarity of sequencing data. We developed a new R package, sourmashconsumr, that lets a wider range of users easily load, analyze, and visualize those outputs in R.
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SC
+2
Published: Mar 07, 2023
A workflow orchestration framework can streamline repeatable tasks and make workflows broadly usable. From several options, we chose Nextflow due to the ease of deploying across platforms, vibrant nf-core community, and ability to manage and monitor workflows with Nextflow Tower.
Connections
Supplements (1): Nextflow template v1.1.0 - GitHub
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Published: Mar 11, 2023
How do you approach getting a microbiome set up in a new lab? We’re sharing protocols for how we collected, stocked, and sequenced a set of cheese rind microbiomes and generated a high-quality metagenomics resource for future computational studies.
TR
Published: Apr 11, 2023
We want to swiftly generate genome assemblies and produce quality control statistics to gauge the need for more curation. We built a Nextflow pipeline that assembles Illumina, Nanopore, or PacBio sequencing reads for a single organism and runs QC checks on the resulting assembly.
Connections
Supplements (1): reads2genome v1.0 - GitHub
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+2
Published: May 26, 2023
We want to seamlessly process and summarize metagenomics data from Illumina or Nanopore technologies. We built a Nextflow workflow that handles common metagenomics tasks and produces useful outputs and intuitive visualizations.
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+4
Published: Jul 19, 2023
We sampled cheese microbial communities to discover bacteriophages with unusual genome chemistries. We isolated 114 bacterial host strains and 17 phages, and identified one phage with a probable arabinose hypermodification of hydroxymethylcytosine.
Connections
Supplements (8): Raw short reads from 11 cheese communities and one virome - ENA • Taxonomic and functional analysis - MGnify • Raw long reads from one cheese community - ENA • Serratia phage 92A1, complete genome - GenBank • Arthrobacter phage 1191A, complete genome - GenBank • Phage genomes and host 16S data - Zenodo • Protocol - Enriching and isolating phages on agar plates - protocols.io • Protocol - Enriching and isolating phages in liquid culture - protocols.io
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+4
Published: Jul 20, 2023
Horizontal gene transfer (HGT) is the exchange of DNA between species. It can lead to the acquisition of new gene functions, so finding HGT events can reveal genome novelty. preHGT is a pipeline that uses multiple existing methods to quickly screen for transferred genes.
Connections
Supplements (1): Code v1.0.0 - GitHub
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Published: Aug 15, 2023
Hoping to find proteins that alter physiology in useful ways, we screened venom data sets for toxins fused to domains with additional functionality. We identified candidates, but struggled to infer any novel functions, and none seem well-conserved across venomous species.
Connections
Supplements (2): Code v2.0 - GitHub • Data - Zenodo
