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Fix grammar and clarity in use case examples #151

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stephwon merged 1 commit into from
Mar 30, 2026
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Fix grammar and clarity in use case examples #151

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2 changes: 1 addition & 1 deletion joss/paper.md
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Expand Up @@ -109,7 +109,7 @@ Echinicola & FALSE & 244 & 978 & 0.052885411 \\

We present the three use case examples to demonstrate the application of YACHT for identifying taxonomy in microbiome studies: (i) analyzing low-abundance metagenomic samples that are common in clinical settings, (ii) performing MAG fishing to detect specific metagenomic-assembled genomes, and (iii) evaluating synthetic microbial communities to identify the presence of specific organisms.

**Low abundance samples:** YACHT can analyze metagenomic samples with low microbial DNA concentrations common in clinical and environmental studies. Using a human skin metagenomics samples, we show that ANI threshold and k-size markedly influence species specificity. See [Low abundance samples](https://github.com/KoslickiLab/YACHT/tree/main/use_case_examples/low_abundance_samples).
**Low abundance samples:** YACHT can analyze metagenomic samples with low microbial DNA concentrations common in clinical and environmental studies. Using a human skin metagenomics sample, we show that ANI threshold and k-size markedly influence species specificity. See [Low abundance samples](https://github.com/KoslickiLab/YACHT/tree/main/use_case_examples/low_abundance_samples).

**Metagenomic-assembled genome (MAG) fishing:** Using a single MAG as a training reference database, YACHT searches for specific MAGs within a sample. Applied to two skin metagenomic samples, results shows that detection is sensitive to sequencing depth, coverage, and parameter choice. See [MAG fishing](https://github.com/KoslickiLab/YACHT/tree/main/use_case_examples/MAG_fishing).

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