decontam
decontam copied to clipboard
benjjneb
Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data
I used the "prevalence" method to filter out contaminants. Everything worked fine but the when I graph Prevalence (true samples) aganst Prevelance (Negative Controls) the data does not get properly...
I have a question about using decontam to determine if the lack of complete sterility during collection is skewing the community compositions of my swab samples. My field negatives have...
Hi Benjamin, First of all, I love the idea of statistically removing contaminants and in general, the promotion of including controls in microbial studies. I am struggling a bit with...
Thank you very much for your great work. We are going to perform metagenomic analyses by 16S using human tissue samples. I would like to make sure about "DNA quantitation...
Hello, I have 6 negative controls across extraction batches for about 200 samples - I knew this might be too few negative controls for prevalence filtering in decontam to identify...
We have used the decontam package to identify contaminants from our nasopharyngeal and induced sputum dataset (V4 Illumina MiSeq). Since these are generally low biomass specimens: 1) We only included...
Hi, I'm working with data with loads of human DNA and little, if any, bacterial DNA. To avoid cross-sample contamination, we have performed DNA extraction and library prep alternating a...
Is it necessary that I run decontam separately for different sample types when they all are low-biomass? I have ~300 swab samples from multiple body sites and breast pump equipment...
This program is great! OK, I have identified which sequences are likely contaminants in my samples with the frequency, prevalence, and both methods. I now have a list of sequences...
Dear Benjamin, A big thanks for developing of this program! This tool is very necessary! I would be very glad if you could answer in my questions about using decontam:...
