Merge pull request #65 from smithlabcode/update-adaptor-contaminants

Updating adapter and contaminant files from FastQC v0.12.0

Configuration/adapter_list.txt

@@ -1,26 +1,27 @@
-# This file contains a set of sequence fragments which will be explicitly
-# searched against your library.  The reporting will be similar to the 
-# Kmer plot, except that every sequence in this list will be shown so 
-# you can use this to judge the level of adapter read-through even if those
-# adapter sequences aren't picked out by the Kmer module.
-#
-# Since every sequence here will be analysed and the results plotted it 
-# doesn't make any sense to include duplicate sequences, or to add too
-# many sequences since your plot will end up a mess.
-#
-# You can add more sequences to the file by putting one line per entry
-# and specifying a name[tab]sequence.  If the contaminant you add is 
-# likely to be of use to others please consider sending it to the FastQ
-# authors, either via a bug report at www.bioinformatics.babraham.ac.uk/bugzilla/
-# or by directly emailing simon.andrews@babraham.ac.uk so other users of
-# the program can benefit.
-#
-# For the time being it's going to be easier to interpret this plot if all
-# of the sequences provided are the same length, so we've gone with 12bp
-# fragments for now.
-
-Illumina Universal Adapter					AGATCGGAAGAG
-Illumina Small RNA 3 prime Adapter				TGGAATTCTCGG
-Illumina Small RNA 5 prime Adapter				GATCGTCGGACT
-Nextera Transposase Sequence				CTGTCTCTTATA
-SOLID Small RNA Adapter						CGCCTTGGCCGT
+# This file contains a set of sequence fragments which will be explicitly
+# searched against your library.  The reporting will be similar to the 
+# Kmer plot, except that every sequence in this list will be shown so 
+# you can use this to judge the level of adapter read-through even if those
+# adapter sequences aren't picked out by the Kmer module.
+#
+# Since every sequence here will be analysed and the results plotted it 
+# doesn't make any sense to include duplicate sequences, or to add too
+# many sequences since your plot will end up a mess.
+#
+# You can add more sequences to the file by putting one line per entry
+# and specifying a name[tab]sequence.  If the contaminant you add is 
+# likely to be of use to others please consider sending it to the FastQ
+# authors, either via a bug report at www.bioinformatics.babraham.ac.uk/bugzilla/
+# or by directly emailing simon.andrews@babraham.ac.uk so other users of
+# the program can benefit.
+#
+# For the time being it's going to be easier to interpret this plot if all
+# of the sequences provided are the same length, so we've gone with 12bp
+# fragments for now.
+
+Illumina Universal Adapter					AGATCGGAAGAG
+Illumina Small RNA 3' Adapter				TGGAATTCTCGG
+Illumina Small RNA 5' Adapter				GATCGTCGGACT
+Nextera Transposase Sequence				CTGTCTCTTATA
+PolyA										AAAAAAAAAAAA
+PolyG										GGGGGGGGGGGG