Will’s Public NAO Notebook

Re-analysis of Crits-Christoph et al. (2021) using pipeline v2.4.0

Profiling the v2 index workflow

Breaking down the computational costs

Investigating the v2 pipeline’s human-virus assignment behavior

Checking treatment of partially-human-infecting virus taxa

Setting up AWS Batch to work with the NAO’s MGS workflow

A hopefully-simple guide to an unfortunately-complicated service.

Workflow analysis of Munk et al. (2022)

A global wastewater study.

Workflow analysis of Ng et al. (2019)

Wastewater from Singapore.

Workflow analysis of Bengtsson-Palme et al. (2016)

Wastewater grab samples from Sweden.

Workflow analysis of Maritz et al. (2019)

Wastewater from NYC.

Workflow analysis of Brinch et al. (2020)

Wastewater from Copenhagen.

Workflow analysis of Leung et al. (2021)

Air sampling from urban public transit systems.

Workflow analysis of Rosario et al. (2018)

Air sampling from a student dorm in Colorado.

Workflow analysis of Prussin et al. (2019)

Air filters from a daycare in Virginia.

Workflow analysis of Brumfield et al. (2022)

Wastewater from a manhole in Maryland.

Workflow analysis of Spurbeck et al. (2023)

Followup analysis of Yang et al. (2020)

Digging into deduplication.

Workflow analysis of Yang et al. (2020)

Wastewater from Xinjiang.

Improving read deduplication in the MGS workflow

Removing reverse-complement duplicates of human-viral reads.

Workflow analysis of Rothman et al. (2021), part 2

Panel-enriched samples.

Workflow analysis of Rothman et al. (2021), part 1

Unenriched samples.

Workflow analysis of Crits-Christoph et al. (2021), part 3

Fixing the virus pipeline.

Workflow analysis of Crits-Christoph et al. (2021), part 2

Abundance and composition of human-infecting viruses.

Workflow analysis of Crits-Christoph et al. (2021), part 1

Preprocessing and composition.

Automating BLAST validation of human viral read assignment

Experiments with BLASTN remote mode

Project Runway RNA-seq testing data: removing livestock reads

Workflow analysis of Project Runway RNA-seq testing data

Applying a new workflow to some oldish data.

Estimating the effect of read depth on duplication rate for Project Runway DNA data

How deep can we go?

Comparing viral read assignments between pipelines on Project Runway data

Initial analysis of Project Runway protocol testing data

Comparing options for read deduplication

Clumpify vs fastp

Comparing Ribodetector and bbduk for rRNA detection

In search of quick rRNA filtering.

Comparing FASTP and AdapterRemoval for MGS pre-processing

Two tools – how do they perform?

How does Element AVITI sequencing work?

Findings of a shallow investigation

Extraction experiment 2: high-level results & interpretation

Comparing RNA yields and quality across extraction kits for settled solids