Will’s Public NAO Notebook
Profiling the v2 index workflow
Breaking down the computational costs
Jul 18, 2024
Investigating the v2 pipeline’s human-virus assignment behavior
Checking treatment of partially-human-infecting virus taxa
Jul 1, 2024
Setting up AWS Batch to work with the NAO’s MGS workflow
A hopefully-simple guide to an unfortunately-complicated service.
Jun 11, 2024
Workflow analysis of Munk et al. (2022)
A global wastewater study.
May 7, 2024
Workflow analysis of Ng et al. (2019)
Wastewater from Singapore.
May 1, 2024
Workflow analysis of Bengtsson-Palme et al. (2016)
Wastewater grab samples from Sweden.
May 1, 2024
Workflow analysis of Maritz et al. (2019)
Wastewater from NYC.
May 1, 2024
Workflow analysis of Brinch et al. (2020)
Wastewater from Copenhagen.
Apr 30, 2024
Workflow analysis of Leung et al. (2021)
Air sampling from urban public transit systems.
Apr 19, 2024
Workflow analysis of Rosario et al. (2018)
Air sampling from a student dorm in Colorado.
Apr 12, 2024
Workflow analysis of Prussin et al. (2019)
Air filters from a daycare in Virginia.
Apr 12, 2024
Workflow analysis of Brumfield et al. (2022)
Wastewater from a manhole in Maryland.
Apr 8, 2024
Workflow analysis of Spurbeck et al. (2023)
Cave carpa.
Apr 1, 2024
Followup analysis of Yang et al. (2020)
Digging into deduplication.
Mar 19, 2024
Workflow analysis of Yang et al. (2020)
Wastewater from Xinjiang.
Mar 16, 2024
Improving read deduplication in the MGS workflow
Removing reverse-complement duplicates of human-viral reads.
Mar 1, 2024
Workflow analysis of Rothman et al. (2021), part 2
Panel-enriched samples.
Feb 29, 2024
Workflow analysis of Rothman et al. (2021), part 1
Unenriched samples.
Feb 27, 2024
Workflow analysis of Crits-Christoph et al. (2021), part 3
Fixing the virus pipeline.
Feb 15, 2024
Workflow analysis of Crits-Christoph et al. (2021), part 2
Abundance and composition of human-infecting viruses.
Feb 8, 2024
Workflow analysis of Crits-Christoph et al. (2021), part 1
Preprocessing and composition.
Feb 4, 2024
Automating BLAST validation of human viral read assignment
Experiments with BLASTN remote mode
Jan 30, 2024
Project Runway RNA-seq testing data: removing livestock reads
Dec 22, 2023
Workflow analysis of Project Runway RNA-seq testing data
Applying a new workflow to some oldish data.
Dec 19, 2023
Estimating the effect of read depth on duplication rate for Project Runway DNA data
How deep can we go?
Nov 8, 2023
Comparing viral read assignments between pipelines on Project Runway data
Nov 2, 2023
Initial analysis of Project Runway protocol testing data
Oct 31, 2023
Comparing options for read deduplication
Clumpify vs fastp
Oct 19, 2023
Comparing Ribodetector and bbduk for rRNA detection
In search of quick rRNA filtering.
Oct 16, 2023
Comparing FASTP and AdapterRemoval for MGS pre-processing
Two tools – how do they perform?
Oct 12, 2023
How does Element AVITI sequencing work?
Findings of a shallow investigation
Oct 11, 2023
Extraction experiment 2: high-level results & interpretation
Comparing RNA yields and quality across extraction kits for settled solids
Sep 21, 2023
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