From 59d48fb938b34bf6b51558b6d21ffee98dd38b57 Mon Sep 17 00:00:00 2001 From: Pepijn Kooij Date: Sun, 25 May 2025 13:41:03 -0300 Subject: [PATCH] Update adapters.py new chemistry Added adapter sequences for V14 chemistry, Last updated: 25/11/2024, https://nanoporetech.com/document/chemistry-technical-document#adapter-sequences --- porechop/adapters.py | 34 ++++++++++++++++++++++++++++++++-- 1 file changed, 32 insertions(+), 2 deletions(-) diff --git a/porechop/adapters.py b/porechop/adapters.py index dce7a4f..0fe433d 100644 --- a/porechop/adapters.py +++ b/porechop/adapters.py @@ -78,7 +78,6 @@ 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')), @@ -86,7 +85,6 @@ def get_barcode_name(self): 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')), @@ -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'),