diff --git a/porechop/adapters.py b/porechop/adapters.py index 8c5baa1..e891301 100644 --- a/porechop/adapters.py +++ b/porechop/adapters.py @@ -87,17 +87,19 @@ def get_barcode_name(self): start_sequence=('SQK-MAP006_Short_Y_Top_LI32', 'CGGCGTCTGCTTGGGTGTTTAACCT'), end_sequence= ('SQK-MAP006_Short_Y_Bottom_LI33', 'GGTTAAACACCCAAGCAGACGCCG')), + + # The PCR adapters are used both in PCR DNA kits and some cDNA kits. Adapter('PCR adapters 1', start_sequence=('PCR_1_start', 'ACTTGCCTGTCGCTCTATCTTC'), - end_sequence= ('PCR_1_end', 'GAAGATAGAGCGACAGGCAAGT')), + end_sequence= ('PCR_1_end', 'GAAGATAGAGCGACAGGCAAGT')), - Adapter('PCR tail 1', - start_sequence=('PCR_tail_1_start', 'TTAACCTTTCTGTTGGTGCTGATATTGC'), - end_sequence= ('PCR_tail_1_end', 'GCAATATCAGCACCAACAGAAAGGTTAA')), + Adapter('PCR adapters 2', + start_sequence=('PCR_2_start', 'TTTCTGTTGGTGCTGATATTGC'), + end_sequence= ('PCR_2_end', 'GCAATATCAGCACCAACAGAAA')), - Adapter('PCR tail 2', - start_sequence=('PCR_tail_2_start', 'TTAACCTACTTGCCTGTCGCTCTATCTTC'), - end_sequence= ('PCR_tail_2_end', 'GAAGATAGAGCGACAGGCAAGTAGGTTAA')), + Adapter('PCR adapters 3', + start_sequence=('PCR_3_start', 'TACTTGCCTGTCGCTCTATCTTC'), + end_sequence= ('PCR_3_end', 'GAAGATAGAGCGACAGGCAAGTA')), # 1D^2 kit adapters are interesting. ONT provided the following sequences on their site: @@ -117,6 +119,20 @@ def get_barcode_name(self): # adapter sequences here. + Adapter('Direct RNA RTA', + start_sequence=('DRS_RTA_start', 'GGCTTCTTCTTGCTCTTAGGTAGTAGGTTC'), + end_sequence=('DRS_RTA_end', 'GAGGCGAGCGGTCAATTTTCCTAAGAGCAAGAAGAAGCCTTTTTTTTTT')), + + Adapter('Direct RNA RMX', + start_sequence=('DRS_RMX_start', 'TGATGATGAGGGATAGACGATGGTTGTTTCTGTTGGTGCTGATATTGCTTTTTTTTTTTTTATGATGCAAGATACGCAC'), + end_sequence=('DRS_RMX_end', 'GAGGCGAGCGGTCAATTTGCAATATCAGCACCAACAGAAACAACCATCGTCTATCCCTCATCATCAGAACCTACTA')), + + + Adapter('cDNA SSP', + start_sequence=('cDNA_SSP', 'TTTCTGTTGGTGCTGATATTGCTGCCATTACGGCCGGG'), + end_sequence= ('cDNA_SSP_rev', 'CCCGGCCGTAATGGCAGCAATATCAGCACCAACAGAAA')), + + # Some barcoding kits (like the native barcodes) use the rev comp barcode at the start # of the read and the forward barcode at the end of the read. Adapter('Barcode 1 (reverse)', diff --git a/porechop/version.py b/porechop/version.py index 7ee7940..3be3007 100644 --- a/porechop/version.py +++ b/porechop/version.py @@ -2,4 +2,4 @@ The version is stored here in a separate file so it can exist in only one place. http://stackoverflow.com/questions/458550 """ -__version__ = '0.2.3' +__version__ = '0.2.4-beta'