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Update adapters.py new chemistry #103

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34 changes: 32 additions & 2 deletions porechop/adapters.py
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Original file line number Diff line number Diff line change
Expand Up @@ -78,15 +78,13 @@ def get_barcode_name(self):
start_sequence=('SQK-NSK007_Y_Top', 'AATGTACTTCGTTCAGTTACGTATTGCT'),
end_sequence=('SQK-NSK007_Y_Bottom', 'GCAATACGTAACTGAACGAAGT')),


Adapter('Rapid',
start_sequence=('Rapid_adapter',
'GTTTTCGCATTTATCGTGAAACGCTTTCGCGTTTTTCGTGCGCCGCTTCA')),

Adapter('RBK004_upstream',
start_sequence=('RBK004_upstream', 'AATGTACTTCGTTCAGTTACGGCTTGGGTGTTTAACC')),


Adapter('SQK-MAP006',
start_sequence=('SQK-MAP006_Y_Top_SK63', 'GGTTGTTTCTGTTGGTGCTGATATTGCT'),
end_sequence= ('SQK-MAP006_Y_Bottom_SK64', 'GCAATATCAGCACCAACAGAAA')),
Expand All @@ -95,7 +93,39 @@ def get_barcode_name(self):
start_sequence=('SQK-MAP006_Short_Y_Top_LI32', 'CGGCGTCTGCTTGGGTGTTTAACCT'),
end_sequence= ('SQK-MAP006_Short_Y_Bottom_LI33', 'GGTTAAACACCCAAGCAGACGCCG')),

# New chemistry V14, Last updated: 25/11/2024, https://nanoporetech.com/document/chemistry-technical-document#adapter-sequences
Adapter('Ligation Adapter LA',
start_sequence=('LA_Top', 'TTTTTTTTCCTGTACTTCGTTCAGTTACGTATTGCT'),
end_sequence=('LA_Bottom', 'GCAATACGTAACTGAACGAAGTACAGG')),

Adapter('Native Adapter NA',
start_sequence=('NA_Top', 'TTTTTTTTCCTGTACTTCGTTCAGTTACGTATTGCT'),
end_sequence=('NA_Bottom', 'ACGTAACTGAACGAAGTACAGG')),

Adapter('cDNA Primer cPRM',
start_sequence=('cPRM_Forward', 'ATCGCCTACCGTGACAAGAAAGTTGTCGGTGTCTTTGTGACTTGCCTGTCGCTCTATCTTC'),
end_sequence=('cPRM_Reverse', 'ATCGCCTACCGTGACAAGAAAGTTGTCGGTGTCTTTGTGTTTCTGTTGGTGCTGATATTGC')),

Adapter('Rapid Adapter RA',
start_sequence=('RA_TOP',
'TTTTTTTTCCTGTACTTCGTTCAGTTACGTATTGCT')),

Adapter('RT Primer RTP',
start_sequence=('RTP',
'CTTGCCTGTCGCTCTATCTTCAGAGGAG')),

Adapter('Strand Switching Primer II SSPII',
start_sequence=('SSPII',
'TTTCTGTTGGTGCTGATATTGCTTTVVVVTTVVVVTTVVVVTTVVVVTTTmGmGmG')),

Adapter('cDNA RT Adapter CRTA',
start_sequence=('CRTA',
'CTTGCGGGCGGCGGACTCTCCTCTGAAGATAGAGCGACAGGCAAG')),

Adapter('Rapid Adapter T RAP T',
start_sequence=('RAP_T',
'TTTTTTTTCCTGTACTTCGTTCAGTTACGTATTGCT')),

# The PCR adapters are used both in PCR DNA kits and some cDNA kits.
Adapter('PCR adapters 1',
start_sequence=('PCR_1_start', 'ACTTGCCTGTCGCTCTATCTTC'),
Expand Down