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Created Apr 12, 2022
Published: May 31, 2022
Researchers studying any organism with genomic data can follow this simple walkthrough to create sets of barcoded probes for the multiplexed FISH technique called MERFISH. We’re sharing interactive code notebooks that can be adapted to design barcoded FISH probes for any species.
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Published: Aug 23, 2022
Cells can be highly motile, moving in and out of a microscope’s field of view. Understanding complex life cycles is difficult without continuous observation. To overcome this challenge, we’ve developed a 3D-printed microchamber device to confine cells for long-term visualization.
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Supplements (2): 3D-printing files - NIH 3D Print Exchange • Code v1.1 - GitHub
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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.
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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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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 PacBio HiFi reads from a single organism and runs QC checks on the resulting assembly.
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Supplements (1): Code v1.2 - GitHub
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Published: May 03, 2023
Constraining motile microorganisms for live imaging often requires costly microfluidics or optical traps to keep them in view. We used patterned stamps and agar to make versatile, inexpensive “microchambers” and offer a way to predict the right chamber size for a given organism.
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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.
