Mercurial > repos > iuc > decontam
changeset 3:871214ac722e draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontam commit 8eca6c026e7bd7ab2e471485cb93b8dee1cd2c07
| author | iuc |
|---|---|
| date | Sun, 09 Mar 2025 19:27:13 +0000 |
| parents | 356bec18c68d |
| children | |
| files | decontam.xml |
| diffstat | 1 files changed, 13 insertions(+), 0 deletions(-) [+] |
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--- a/decontam.xml Mon Dec 09 16:04:03 2024 +0000 +++ b/decontam.xml Sun Mar 09 19:27:13 2025 +0000 @@ -1,4 +1,5 @@ <tool id="decontam" name="Decontam" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description>Identification and removal of contaminants</description> <macros> <import>macros.xml</import> </macros> @@ -150,6 +151,18 @@ Currently, only the negative control sample method is implemented in this wrapper. +**Method** + +To identify contaminants decontam requires a defined set of “negative control” samples in + which sequencing was performed on blanks without any biological sample added. +Extraction controls are preferred, and in amplicon sequencing the negative controls + should also be carried through the PCR step, as each step in the workflow + has the potential to introduce new contaminants. + +Decontam then uses Fisher’s exact tests to detect weather a feature is a contaminant or not, +by comparing true samples to ngeative controls. For more details on the detection method see +the publication of decontam. + **Output** - If a phyloseq object is provided as input, the output will be a phyloseq