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Hi there,
I am seeing very low mapping rates (~10-15%) for my whole genome sequencing data using Kraken 2. Samples are gut microbiome samples from patients with heart disease, sequenced on Illumina…
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GTDB-Tk was run using the following shell script:
`/storage1/data19/Gut_Microbiome_Clostridium_scindens/run_gtdbtk_UHGG.sh`
The exact command to run GTDB-Tk was:
`gtdbtk classify_wf -x fasta --cpus 2…
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Microbiome analysis reveals gut microbiota alteration of early-weaned Yimeng black goats with the effect of milk replacer and age
https://pubmed.ncbi.nlm.nih.gov/33789672/
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Hi,
Thank you for a great resource for CAZyme annotation and substrate prediction. I was wondering since the annotation is trained on human gut microbiome (GMGC), would you recommend running it on …
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NTR: microbiome sequencing design
definition: The microbiome comprises all of the genetic material within a microbiota (the entire collection of microorganisms in a specific niche, such as the human …
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GTDB-Tk was run using the following shell script:
`/storage1/data19/Gut_Microbiome_Clostridium_scindens/run_gtdbtk_segata.sh`
The command used to run GTDB-Tk in the shell script was:
`gtdbtk classify…
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Dear author,
Thanks for your excellent work. I have some VLP enrichment samples from the animal gut. When I use the tool, how to select the parameter "--enrichment_preset". The default is "human",…
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Characteristics and Correlations of the Oral and Gut Fungal Microbiome with Hypertension - Chen et al - Microbiol Spectr.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9927468/
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Turnbaugh, P. J.
Ridaura, V. K.
Faith, J. J.
Rey, F. E.
Knight, R.
Gordon, J. I.
2009.
The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice
http://dx.d…
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Gut Microbiome Alterations following Postnatal Iron Supplementation Depend on Iron Form and Persist into Adulthood - McMillen et al - Nutrients
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8838803/