diff --git a/tools/dada2/dada2_assignTaxonomyAddspecies.xml b/tools/dada2/dada2_assignTaxonomyAddspecies.xml
index 4f9eba0cc90..2b8df3af448 100644
--- a/tools/dada2/dada2_assignTaxonomyAddspecies.xml
+++ b/tools/dada2/dada2_assignTaxonomyAddspecies.xml
@@ -172,7 +172,7 @@ taxonomic level"/>
-
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diff --git a/tools/dada2/dada2_primercheck.xml b/tools/dada2/dada2_primercheck.xml
new file mode 100644
index 00000000000..6b90239a256
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+++ b/tools/dada2/dada2_primercheck.xml
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+ macros.xml
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+df <- NULL;
+#for $i, $read in enumerate($paired_cond.reads):
+ #set elid = re.sub('[^\w\-\.]', '_', str($read.element_identifier))
+ #if $paired_cond.paired_select == "single"
+ #set fwd_reads = $read
+ #elif $paired_cond.paired_select == "separate"
+ #set fwd_reads = $read
+ #set rev_reads = $paired_cond.sdaer[i]
+ #else
+ #set fwd_reads = $read.forward
+ #set rev_reads = $read.reverse
+ #end if
+ df <- rbind(df, c('$elid', 'FWD', 'FWD', sapply(FWD.orients, primerHits, fn = '$fwd_reads')))
+ df <- rbind(df, c('$elid', 'REV', 'FWD', sapply(REV.orients, primerHits, fn = '$fwd_reads')))
+ #if $paired_cond.paired_select != "single"
+ #if $paired_cond.paired_select == "separate"
+ #set elid = re.sub('[^\w\-\.]', '_', str($paired_cond.sdaer[i].element_identifier))
+ #end if
+ df <- rbind(df, c('$elid', 'FWD', 'REV', sapply(FWD.orients, primerHits, fn = '$rev_reads')))
+ df <- rbind(df, c('$elid', 'REV', 'REV', sapply(REV.orients, primerHits, fn = '$rev_reads')))
+ #end if
+#end for
+colnames(df) <- c('Sample', 'Primer', 'ReadDir', 'Sequence', 'Complement', 'Reverse', 'RevComp')
+write.table(df, "$out", quote=F, sep="\t", row.names = F, col.names = T)
+ ]]>
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diff --git a/tools/dada2/dada2_removeBimeraDenovo.xml b/tools/dada2/dada2_removeBimeraDenovo.xml
index 55cbe762a6c..a81002e3124 100644
--- a/tools/dada2/dada2_removeBimeraDenovo.xml
+++ b/tools/dada2/dada2_removeBimeraDenovo.xml
@@ -100,7 +100,10 @@ Details
The frequency of chimeric sequences varies substantially from dataset to dataset, and depends on on factors including experimental procedures and sample complexity. Here chimeras make up about 21% of the merged sequence variants, but when we account for the abundances of those variants we see they account for only about 4% of the merged sequence reads.
-Considerations for your own data: Most of your reads should remain after chimera removal (it is not uncommon for a majority of sequence variants to be removed though). If most of your reads were removed as chimeric, upstream processing may need to be revisited. In almost all cases this is caused by primer sequences with ambiguous nucleotides that were not removed prior to beginning the DADA2 pipeline.
+Considerations for your own data: Most of your reads should remain after chimera removal (it is not uncommon for a majority of sequence variants to be removed though). If most of your reads were removed as chimeric, upstream processing may need to be revisited.
+In almost all cases this is caused by primer sequences with ambiguous nucleotides that were not removed prior to beginning the DADA2 pipeline.
+You can check for present primer sequences with the tool `dada2: primer check`
+
@HELP_OVERVIEW@
]]>