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adapters_custom.py
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"""
Copyright 2017 Ryan Wick (rrwick@gmail.com)
https://github.com/rrwick/Porechop
This module contains the class and sequences for known adapters used in Oxford Nanopore library
preparation kits.
This file is part of Porechop. Porechop is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by the Free Software Foundation,
either version 3 of the License, or (at your option) any later version. Porechop is distributed in
the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
details. You should have received a copy of the GNU General Public License along with Porechop. If
not, see <http://www.gnu.org/licenses/>.
"""
import copy
from pathlib import Path
class Adapter(object):
def __init__(self, name, start_sequence=None, end_sequence=None, both_ends_sequence=None):
self.name = name
self.start_sequence = start_sequence if start_sequence else []
self.end_sequence = end_sequence if end_sequence else []
if both_ends_sequence:
self.start_sequence = both_ends_sequence
self.end_sequence = both_ends_sequence
self.best_start_score, self.best_end_score = 0.0, 0.0
def best_start_or_end_score(self):
return max(self.best_start_score, self.best_end_score)
def is_barcode(self):
return self.name.startswith('Barcode ')
def barcode_direction(self):
if '_rev' in self.start_sequence[0]:
return 'reverse'
else:
return 'forward'
def get_barcode_name(self):
"""
Gets the barcode name for the output files. We want a concise name, so it looks at all
options and chooses the shortest.
"""
possible_names = [self.name]
if self.start_sequence:
possible_names.append(self.start_sequence[0])
if self.end_sequence:
possible_names.append(self.end_sequence[0])
barcode_name = sorted(possible_names, key=lambda x: len(x))[0]
return barcode_name.replace(' ', '_')
@classmethod
def from_fasta(cls,
fasta_file,
prefix='',
suffix='',
trim_start=0,
trim_end=0):
fasta_file = Path(fasta_file)
adapter_set_name = fasta_file.stem
with open(fasta_file) as handle:
# Split the file on '>' and remove the first element, which is empty
seqeunces = handle.read().split('>')[1:]
# ensure that the file contains 1 or 2 sequences
assert len(seqeunces) in {1, 2}, f'Adapter fasta file must contain 1 or 2 (start and end) sequences ({fasta_file.stem} contains {len(seqeunces)}'
adapters = []
for s in seqeunces:
name, sequence = s.split('\n', 1)
name = name.strip()
sequence = sequence.replace('\n', '')
adapters.append((name, sequence))
if len(adapters) == 1:
adapter = cls(adapter_set_name,
start_sequence=(adapters[0][0], adapters[0][1]))
elif len(adapters) == 2:
adapter = cls(adapter_set_name,
start_sequence=(adapters[0][0], adapters[0][1]),
end_sequence=(adapters[1][0], adapters[1][1]))
adapter.name = f'{prefix}{adapter.name}{suffix}'
return adapter
# INSTRUCTIONS FOR ADDING CUSTOM ADAPTERS
# ---------------------------------------
# If you need Porechop to remove adapters that aren't included, you can add your own my modifying
# the ADAPTERS list below.
#
# Here is the format for a normal adapter:
# Adapter('Adapter_set_name',
# start_sequence=('Start_adapter_name', 'AAAACCCCGGGGTTTTAAAACCCCGGGGTTTT'),
# end_sequence=('End_adapter_name', 'AACCGGTTAACCGGTTAACCGGTTAACCGGTT'))
#
# You can exclude start_sequence and end_sequence as appropriate.
#
# If you have custom Barcodes, make sure that the adapter set name starts with 'Barcode '. Also,
# remove the existing barcode sequences from this file to avoid conflicts:
# Adapter('Barcode 1',
# start_sequence=('Barcode_1_start', 'AAAAAAAACCCCCCCCGGGGGGGGTTTTTTTT'),
# end_sequence=('Barcode_1_end', 'AAAAAAAACCCCCCCCGGGGGGGGTTTTTTTT')),
# Adapter('Barcode 2',
# start_sequence=('Barcode_2_start', 'TTTTTTTTGGGGGGGGCCCCCCCCAAAAAAAA'),
# end_sequence=('Barcode_2_end', 'TTTTTTTTGGGGGGGGCCCCCCCCAAAAAAAA'))
ADAPTERS = [Adapter('SQK-NSK007',
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')),
Adapter('SQK-MAP006 short',
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')),
Adapter('PCR adapters 2',
start_sequence=('PCR_2_start', 'TTTCTGTTGGTGCTGATATTGC'),
end_sequence=('PCR_2_end', 'GCAATATCAGCACCAACAGAAA')),
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:
# start: GGCGTCTGCTTGGGTGTTTAACCTTTTTGTCAGAGAGGTTCCAAGTCAGAGAGGTTCCT
# end: GGAACCTCTCTCTGACTTGGAACCTCTCTGACAAAAAGGTTAAACACCCAAGCAGACGCCAGCAAT
# But when looking at actual reads, I found two parts. The first corresponds to one end
# of the provided sequences (through slightly different):
Adapter('1D^2 part 1',
start_sequence=('1D2_part_1_start', 'GAGAGGTTCCAAGTCAGAGAGGTTCCT'),
end_sequence=('1D2_part_1_end', 'AGGAACCTCTCTGACTTGGAACCTCTC')),
# and the second part corresponds to the other end, combined with a bit of standard 1D
# adapter:
Adapter('1D^2 part 2',
start_sequence=('1D2_part_2_start', 'CTTCGTTCAGTTACGTATTGCTGGCGTCTGCTT'),
end_sequence=('1D2_part_2_end', 'CACCCAAGCAGACGCCAGCAATACGTAACT')),
# The middle part of the provided sequences is less common, so I've left it out of the
# adapter sequences here.
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)',
start_sequence=('BC01_rev', 'CACAAAGACACCGACAACTTTCTT'),
end_sequence=('BC01', 'AAGAAAGTTGTCGGTGTCTTTGTG')),
Adapter('Barcode 2 (reverse)',
start_sequence=('BC02_rev', 'ACAGACGACTACAAACGGAATCGA'),
end_sequence=('BC02', 'TCGATTCCGTTTGTAGTCGTCTGT')),
Adapter('Barcode 3 (reverse)',
start_sequence=('BC03_rev', 'CCTGGTAACTGGGACACAAGACTC'),
end_sequence=('BC03', 'GAGTCTTGTGTCCCAGTTACCAGG')),
Adapter('Barcode 4 (reverse)',
start_sequence=('BC04_rev', 'TAGGGAAACACGATAGAATCCGAA'),
end_sequence=('BC04', 'TTCGGATTCTATCGTGTTTCCCTA')),
Adapter('Barcode 5 (reverse)',
start_sequence=('BC05_rev', 'AAGGTTACACAAACCCTGGACAAG'),
end_sequence=('BC05', 'CTTGTCCAGGGTTTGTGTAACCTT')),
Adapter('Barcode 6 (reverse)',
start_sequence=('BC06_rev', 'GACTACTTTCTGCCTTTGCGAGAA'),
end_sequence=('BC06', 'TTCTCGCAAAGGCAGAAAGTAGTC')),
Adapter('Barcode 7 (reverse)',
start_sequence=('BC07_rev', 'AAGGATTCATTCCCACGGTAACAC'),
end_sequence=('BC07', 'GTGTTACCGTGGGAATGAATCCTT')),
Adapter('Barcode 8 (reverse)',
start_sequence=('BC08_rev', 'ACGTAACTTGGTTTGTTCCCTGAA'),
end_sequence=('BC08', 'TTCAGGGAACAAACCAAGTTACGT')),
Adapter('Barcode 9 (reverse)',
start_sequence=('BC09_rev', 'AACCAAGACTCGCTGTGCCTAGTT'),
end_sequence=('BC09', 'AACTAGGCACAGCGAGTCTTGGTT')),
Adapter('Barcode 10 (reverse)',
start_sequence=('BC10_rev', 'GAGAGGACAAAGGTTTCAACGCTT'),
end_sequence=('BC10', 'AAGCGTTGAAACCTTTGTCCTCTC')),
Adapter('Barcode 11 (reverse)',
start_sequence=('BC11_rev', 'TCCATTCCCTCCGATAGATGAAAC'),
end_sequence=('BC11', 'GTTTCATCTATCGGAGGGAATGGA')),
Adapter('Barcode 12 (reverse)',
start_sequence=('BC12_rev', 'TCCGATTCTGCTTCTTTCTACCTG'),
end_sequence=('BC12', 'CAGGTAGAAAGAAGCAGAATCGGA')),
# Other barcoding kits (like the PCR and rapid barcodes) use the forward barcode at the
# start of the read and the rev comp barcode at the end of the read.
Adapter('Barcode 1 (forward)',
start_sequence=('BC01', 'AAGAAAGTTGTCGGTGTCTTTGTG'),
end_sequence=('BC01_rev', 'CACAAAGACACCGACAACTTTCTT')),
Adapter('Barcode 2 (forward)',
start_sequence=('BC02', 'TCGATTCCGTTTGTAGTCGTCTGT'),
end_sequence=('BC02_rev', 'ACAGACGACTACAAACGGAATCGA')),
Adapter('Barcode 3 (forward)',
start_sequence=('BC03', 'GAGTCTTGTGTCCCAGTTACCAGG'),
end_sequence=('BC03_rev', 'CCTGGTAACTGGGACACAAGACTC')),
Adapter('Barcode 4 (forward)',
start_sequence=('BC04', 'TTCGGATTCTATCGTGTTTCCCTA'),
end_sequence=('BC04_rev', 'TAGGGAAACACGATAGAATCCGAA')),
Adapter('Barcode 5 (forward)',
start_sequence=('BC05', 'CTTGTCCAGGGTTTGTGTAACCTT'),
end_sequence=('BC05_rev', 'AAGGTTACACAAACCCTGGACAAG')),
Adapter('Barcode 6 (forward)',
start_sequence=('BC06', 'TTCTCGCAAAGGCAGAAAGTAGTC'),
end_sequence=('BC06_rev', 'GACTACTTTCTGCCTTTGCGAGAA')),
Adapter('Barcode 7 (forward)',
start_sequence=('BC07', 'GTGTTACCGTGGGAATGAATCCTT'),
end_sequence=('BC07_rev', 'AAGGATTCATTCCCACGGTAACAC')),
Adapter('Barcode 8 (forward)',
start_sequence=('BC08', 'TTCAGGGAACAAACCAAGTTACGT'),
end_sequence=('BC08_rev', 'ACGTAACTTGGTTTGTTCCCTGAA')),
Adapter('Barcode 9 (forward)',
start_sequence=('BC09', 'AACTAGGCACAGCGAGTCTTGGTT'),
end_sequence=('BC09_rev', 'AACCAAGACTCGCTGTGCCTAGTT')),
Adapter('Barcode 10 (forward)',
start_sequence=('BC10', 'AAGCGTTGAAACCTTTGTCCTCTC'),
end_sequence=('BC10_rev', 'GAGAGGACAAAGGTTTCAACGCTT')),
Adapter('Barcode 11 (forward)',
start_sequence=('BC11', 'GTTTCATCTATCGGAGGGAATGGA'),
end_sequence=('BC11_rev', 'TCCATTCCCTCCGATAGATGAAAC')),
Adapter('Barcode 12 (forward)',
start_sequence=('BC12', 'CAGGTAGAAAGAAGCAGAATCGGA'),
end_sequence=('BC12_rev', 'TCCGATTCTGCTTCTTTCTACCTG')),
Adapter('Barcode 13 (forward)',
start_sequence=('BC13', 'AGAACGACTTCCATACTCGTGTGA'),
end_sequence=('BC13_rev', 'TCACACGAGTATGGAAGTCGTTCT')),
Adapter('Barcode 14 (forward)',
start_sequence=('BC14', 'AACGAGTCTCTTGGGACCCATAGA'),
end_sequence=('BC14_rev', 'TCTATGGGTCCCAAGAGACTCGTT')),
Adapter('Barcode 15 (forward)',
start_sequence=('BC15', 'AGGTCTACCTCGCTAACACCACTG'),
end_sequence=('BC15_rev', 'CAGTGGTGTTAGCGAGGTAGACCT')),
Adapter('Barcode 16 (forward)',
start_sequence=('BC16', 'CGTCAACTGACAGTGGTTCGTACT'),
end_sequence=('BC16_rev', 'AGTACGAACCACTGTCAGTTGACG')),
Adapter('Barcode 17 (forward)',
start_sequence=('BC17', 'ACCCTCCAGGAAAGTACCTCTGAT'),
end_sequence=('BC17_rev', 'ATCAGAGGTACTTTCCTGGAGGGT')),
Adapter('Barcode 18 (forward)',
start_sequence=('BC18', 'CCAAACCCAACAACCTAGATAGGC'),
end_sequence=('BC18_rev', 'GCCTATCTAGGTTGTTGGGTTTGG')),
Adapter('Barcode 19 (forward)',
start_sequence=('BC19', 'GTTCCTCGTGCAGTGTCAAGAGAT'),
end_sequence=('BC19_rev', 'ATCTCTTGACACTGCACGAGGAAC')),
Adapter('Barcode 20 (forward)',
start_sequence=('BC20', 'TTGCGTCCTGTTACGAGAACTCAT'),
end_sequence=('BC20_rev', 'ATGAGTTCTCGTAACAGGACGCAA')),
Adapter('Barcode 21 (forward)',
start_sequence=('BC21', 'GAGCCTCTCATTGTCCGTTCTCTA'),
end_sequence=('BC21_rev', 'TAGAGAACGGACAATGAGAGGCTC')),
Adapter('Barcode 22 (forward)',
start_sequence=('BC22', 'ACCACTGCCATGTATCAAAGTACG'),
end_sequence=('BC22_rev', 'CGTACTTTGATACATGGCAGTGGT')),
Adapter('Barcode 23 (forward)',
start_sequence=('BC23', 'CTTACTACCCAGTGAACCTCCTCG'),
end_sequence=('BC23_rev', 'CGAGGAGGTTCACTGGGTAGTAAG')),
Adapter('Barcode 24 (forward)',
start_sequence=('BC24', 'GCATAGTTCTGCATGATGGGTTAG'),
end_sequence=('BC24_rev', 'CTAACCCATCATGCAGAACTATGC')),
Adapter('Barcode 25 (forward)',
start_sequence=('BC25', 'GTAAGTTGGGTATGCAACGCAATG'),
end_sequence=('BC25_rev', 'CATTGCGTTGCATACCCAACTTAC')),
Adapter('Barcode 26 (forward)',
start_sequence=('BC26', 'CATACAGCGACTACGCATTCTCAT'),
end_sequence=('BC26_rev', 'ATGAGAATGCGTAGTCGCTGTATG')),
Adapter('Barcode 27 (forward)',
start_sequence=('BC27', 'CGACGGTTAGATTCACCTCTTACA'),
end_sequence=('BC27_rev', 'TGTAAGAGGTGAATCTAACCGTCG')),
Adapter('Barcode 28 (forward)',
start_sequence=('BC28', 'TGAAACCTAAGAAGGCACCGTATC'),
end_sequence=('BC28_rev', 'GATACGGTGCCTTCTTAGGTTTCA')),
Adapter('Barcode 29 (forward)',
start_sequence=('BC29', 'CTAGACACCTTGGGTTGACAGACC'),
end_sequence=('BC29_rev', 'GGTCTGTCAACCCAAGGTGTCTAG')),
Adapter('Barcode 30 (forward)',
start_sequence=('BC30', 'TCAGTGAGGATCTACTTCGACCCA'),
end_sequence=('BC30_rev', 'TGGGTCGAAGTAGATCCTCACTGA')),
Adapter('Barcode 31 (forward)',
start_sequence=('BC31', 'TGCGTACAGCAATCAGTTACATTG'),
end_sequence=('BC31_rev', 'CAATGTAACTGATTGCTGTACGCA')),
Adapter('Barcode 32 (forward)',
start_sequence=('BC32', 'CCAGTAGAAGTCCGACAACGTCAT'),
end_sequence=('BC32_rev', 'ATGACGTTGTCGGACTTCTACTGG')),
Adapter('Barcode 33 (forward)',
start_sequence=('BC33', 'CAGACTTGGTACGGTTGGGTAACT'),
end_sequence=('BC33_rev', 'AGTTACCCAACCGTACCAAGTCTG')),
Adapter('Barcode 34 (forward)',
start_sequence=('BC34', 'GGACGAAGAACTCAAGTCAAAGGC'),
end_sequence=('BC34_rev', 'GCCTTTGACTTGAGTTCTTCGTCC')),
Adapter('Barcode 35 (forward)',
start_sequence=('BC35', 'CTACTTACGAAGCTGAGGGACTGC'),
end_sequence=('BC35_rev', 'GCAGTCCCTCAGCTTCGTAAGTAG')),
Adapter('Barcode 36 (forward)',
start_sequence=('BC36', 'ATGTCCCAGTTAGAGGAGGAAACA'),
end_sequence=('BC36_rev', 'TGTTTCCTCCTCTAACTGGGACAT')),
Adapter('Barcode 37 (forward)',
start_sequence=('BC37', 'GCTTGCGATTGATGCTTAGTATCA'),
end_sequence=('BC37_rev', 'TGATACTAAGCATCAATCGCAAGC')),
Adapter('Barcode 38 (forward)',
start_sequence=('BC38', 'ACCACAGGAGGACGATACAGAGAA'),
end_sequence=('BC38_rev', 'TTCTCTGTATCGTCCTCCTGTGGT')),
Adapter('Barcode 39 (forward)',
start_sequence=('BC39', 'CCACAGTGTCAACTAGAGCCTCTC'),
end_sequence=('BC39_rev', 'GAGAGGCTCTAGTTGACACTGTGG')),
Adapter('Barcode 40 (forward)',
start_sequence=('BC40', 'TAGTTTGGATGACCAAGGATAGCC'),
end_sequence=('BC40_rev', 'GGCTATCCTTGGTCATCCAAACTA')),
Adapter('Barcode 41 (forward)',
start_sequence=('BC41', 'GGAGTTCGTCCAGAGAAGTACACG'),
end_sequence=('BC41_rev', 'CGTGTACTTCTCTGGACGAACTCC')),
Adapter('Barcode 42 (forward)',
start_sequence=('BC42', 'CTACGTGTAAGGCATACCTGCCAG'),
end_sequence=('BC42_rev', 'CTGGCAGGTATGCCTTACACGTAG')),
Adapter('Barcode 43 (forward)',
start_sequence=('BC43', 'CTTTCGTTGTTGACTCGACGGTAG'),
end_sequence=('BC43_rev', 'CTACCGTCGAGTCAACAACGAAAG')),
Adapter('Barcode 44 (forward)',
start_sequence=('BC44', 'AGTAGAAAGGGTTCCTTCCCACTC'),
end_sequence=('BC44_rev', 'GAGTGGGAAGGAACCCTTTCTACT')),
Adapter('Barcode 45 (forward)',
start_sequence=('BC45', 'GATCCAACAGAGATGCCTTCAGTG'),
end_sequence=('BC45_rev', 'CACTGAAGGCATCTCTGTTGGATC')),
Adapter('Barcode 46 (forward)',
start_sequence=('BC46', 'GCTGTGTTCCACTTCATTCTCCTG'),
end_sequence=('BC46_rev', 'CAGGAGAATGAAGTGGAACACAGC')),
Adapter('Barcode 47 (forward)',
start_sequence=('BC47', 'GTGCAACTTTCCCACAGGTAGTTC'),
end_sequence=('BC47_rev', 'GAACTACCTGTGGGAAAGTTGCAC')),
Adapter('Barcode 48 (forward)',
start_sequence=('BC48', 'CATCTGGAACGTGGTACACCTGTA'),
end_sequence=('BC48_rev', 'TACAGGTGTACCACGTTCCAGATG')),
Adapter('Barcode 49 (forward)',
start_sequence=('BC49', 'ACTGGTGCAGCTTTGAACATCTAG'),
end_sequence=('BC49_rev', 'CTAGATGTTCAAAGCTGCACCAGT')),
Adapter('Barcode 50 (forward)',
start_sequence=('BC50', 'ATGGACTTTGGTAACTTCCTGCGT'),
end_sequence=('BC50_rev', 'ACGCAGGAAGTTACCAAAGTCCAT')),
Adapter('Barcode 51 (forward)',
start_sequence=('BC51', 'GTTGAATGAGCCTACTGGGTCCTC'),
end_sequence=('BC51_rev', 'GAGGACCCAGTAGGCTCATTCAAC')),
Adapter('Barcode 52 (forward)',
start_sequence=('BC52', 'TGAGAGACAAGATTGTTCGTGGAC'),
end_sequence=('BC52_rev', 'GTCCACGAACAATCTTGTCTCTCA')),
Adapter('Barcode 53 (forward)',
start_sequence=('BC53', 'AGATTCAGACCGTCTCATGCAAAG'),
end_sequence=('BC53_rev', 'CTTTGCATGAGACGGTCTGAATCT')),
Adapter('Barcode 54 (forward)',
start_sequence=('BC54', 'CAAGAGCTTTGACTAAGGAGCATG'),
end_sequence=('BC54_rev', 'CATGCTCCTTAGTCAAAGCTCTTG')),
Adapter('Barcode 55 (forward)',
start_sequence=('BC55', 'TGGAAGATGAGACCCTGATCTACG'),
end_sequence=('BC55_rev', 'CGTAGATCAGGGTCTCATCTTCCA')),
Adapter('Barcode 56 (forward)',
start_sequence=('BC56', 'TCACTACTCAACAGGTGGCATGAA'),
end_sequence=('BC56_rev', 'TTCATGCCACCTGTTGAGTAGTGA')),
Adapter('Barcode 57 (forward)',
start_sequence=('BC57', 'GCTAGGTCAATCTCCTTCGGAAGT'),
end_sequence=('BC57_rev', 'ACTTCCGAAGGAGATTGACCTAGC')),
Adapter('Barcode 58 (forward)',
start_sequence=('BC58', 'CAGGTTACTCCTCCGTGAGTCTGA'),
end_sequence=('BC58_rev', 'TCAGACTCACGGAGGAGTAACCTG')),
Adapter('Barcode 59 (forward)',
start_sequence=('BC59', 'TCAATCAAGAAGGGAAAGCAAGGT'),
end_sequence=('BC59_rev', 'ACCTTGCTTTCCCTTCTTGATTGA')),
Adapter('Barcode 60 (forward)',
start_sequence=('BC60', 'CATGTTCAACCAAGGCTTCTATGG'),
end_sequence=('BC60_rev', 'CCATAGAAGCCTTGGTTGAACATG')),
Adapter('Barcode 61 (forward)',
start_sequence=('BC61', 'AGAGGGTACTATGTGCCTCAGCAC'),
end_sequence=('BC61_rev', 'GTGCTGAGGCACATAGTACCCTCT')),
Adapter('Barcode 62 (forward)',
start_sequence=('BC62', 'CACCCACACTTACTTCAGGACGTA'),
end_sequence=('BC62_rev', 'TACGTCCTGAAGTAAGTGTGGGTG')),
Adapter('Barcode 63 (forward)',
start_sequence=('BC63', 'TTCTGAAGTTCCTGGGTCTTGAAC'),
end_sequence=('BC63_rev', 'GTTCAAGACCCAGGAACTTCAGAA')),
Adapter('Barcode 64 (forward)',
start_sequence=('BC64', 'GACAGACACCGTTCATCGACTTTC'),
end_sequence=('BC64_rev', 'GAAAGTCGATGAACGGTGTCTGTC')),
Adapter('Barcode 65 (forward)',
start_sequence=('BC65', 'TTCTCAGTCTTCCTCCAGACAAGG'),
end_sequence=('BC65_rev', 'CCTTGTCTGGAGGAAGACTGAGAA')),
Adapter('Barcode 66 (forward)',
start_sequence=('BC66', 'CCGATCCTTGTGGCTTCTAACTTC'),
end_sequence=('BC66_rev', 'GAAGTTAGAAGCCACAAGGATCGG')),
Adapter('Barcode 67 (forward)',
start_sequence=('BC67', 'GTTTGTCATACTCGTGTGCTCACC'),
end_sequence=('BC67_rev', 'GGTGAGCACACGAGTATGACAAAC')),
Adapter('Barcode 68 (forward)',
start_sequence=('BC68', 'GAATCTAAGCAAACACGAAGGTGG'),
end_sequence=('BC68_rev', 'CCACCTTCGTGTTTGCTTAGATTC')),
Adapter('Barcode 69 (forward)',
start_sequence=('BC69', 'TACAGTCCGAGCCTCATGTGATCT'),
end_sequence=('BC69_rev', 'AGATCACATGAGGCTCGGACTGTA')),
Adapter('Barcode 70 (forward)',
start_sequence=('BC70', 'ACCGAGATCCTACGAATGGAGTGT'),
end_sequence=('BC70_rev', 'ACACTCCATTCGTAGGATCTCGGT')),
Adapter('Barcode 71 (forward)',
start_sequence=('BC71', 'CCTGGGAGCATCAGGTAGTAACAG'),
end_sequence=('BC71_rev', 'CTGTTACTACCTGATGCTCCCAGG')),
Adapter('Barcode 72 (forward)',
start_sequence=('BC72', 'TAGCTGACTGTCTTCCATACCGAC'),
end_sequence=('BC72_rev', 'GTCGGTATGGAAGACAGTCAGCTA')),
Adapter('Barcode 73 (forward)',
start_sequence=('BC73', 'AAGAAACAGGATGACAGAACCCTC'),
end_sequence=('BC73_rev', 'GAGGGTTCTGTCATCCTGTTTCTT')),
Adapter('Barcode 74 (forward)',
start_sequence=('BC74', 'TACAAGCATCCCAACACTTCCACT'),
end_sequence=('BC74_rev', 'AGTGGAAGTGTTGGGATGCTTGTA')),
Adapter('Barcode 75 (forward)',
start_sequence=('BC75', 'GACCATTGTGATGAACCCTGTTGT'),
end_sequence=('BC75_rev', 'ACAACAGGGTTCATCACAATGGTC')),
Adapter('Barcode 76 (forward)',
start_sequence=('BC76', 'ATGCTTGTTACATCAACCCTGGAC'),
end_sequence=('BC76_rev', 'GTCCAGGGTTGATGTAACAAGCAT')),
Adapter('Barcode 77 (forward)',
start_sequence=('BC77', 'CGACCTGTTTCTCAGGGATACAAC'),
end_sequence=('BC77_rev', 'GTTGTATCCCTGAGAAACAGGTCG')),
Adapter('Barcode 78 (forward)',
start_sequence=('BC78', 'AACAACCGAACCTTTGAATCAGAA'),
end_sequence=('BC78_rev', 'TTCTGATTCAAAGGTTCGGTTGTT')),
Adapter('Barcode 79 (forward)',
start_sequence=('BC79', 'TCTCGGAGATAGTTCTCACTGCTG'),
end_sequence=('BC79_rev', 'CAGCAGTGAGAACTATCTCCGAGA')),
Adapter('Barcode 80 (forward)',
start_sequence=('BC80', 'CGGATGAACATAGGATAGCGATTC'),
end_sequence=('BC80_rev', 'GAATCGCTATCCTATGTTCATCCG')),
Adapter('Barcode 81 (forward)',
start_sequence=('BC81', 'CCTCATCTTGTGAAGTTGTTTCGG'),
end_sequence=('BC81_rev', 'CCGAAACAACTTCACAAGATGAGG')),
Adapter('Barcode 82 (forward)',
start_sequence=('BC82', 'ACGGTATGTCGAGTTCCAGGACTA'),
end_sequence=('BC82_rev', 'TAGTCCTGGAACTCGACATACCGT')),
Adapter('Barcode 83 (forward)',
start_sequence=('BC83', 'TGGCTTGATCTAGGTAAGGTCGAA'),
end_sequence=('BC83_rev', 'TTCGACCTTACCTAGATCAAGCCA')),
Adapter('Barcode 84 (forward)',
start_sequence=('BC84', 'GTAGTGGACCTAGAACCTGTGCCA'),
end_sequence=('BC84_rev', 'TGGCACAGGTTCTAGGTCCACTAC')),
Adapter('Barcode 85 (forward)',
start_sequence=('BC85', 'AACGGAGGAGTTAGTTGGATGATC'),
end_sequence=('BC85_rev', 'GATCATCCAACTAACTCCTCCGTT')),
Adapter('Barcode 86 (forward)',
start_sequence=('BC86', 'AGGTGATCCCAACAAGCGTAAGTA'),
end_sequence=('BC86_rev', 'TACTTACGCTTGTTGGGATCACCT')),
Adapter('Barcode 87 (forward)',
start_sequence=('BC87', 'TACATGCTCCTGTTGTTAGGGAGG'),
end_sequence=('BC87_rev', 'CCTCCCTAACAACAGGAGCATGTA')),
Adapter('Barcode 88 (forward)',
start_sequence=('BC88', 'TCTTCTACTACCGATCCGAAGCAG'),
end_sequence=('BC88_rev', 'CTGCTTCGGATCGGTAGTAGAAGA')),
Adapter('Barcode 89 (forward)',
start_sequence=('BC89', 'ACAGCATCAATGTTTGGCTAGTTG'),
end_sequence=('BC89_rev', 'CAACTAGCCAAACATTGATGCTGT')),
Adapter('Barcode 90 (forward)',
start_sequence=('BC90', 'GATGTAGAGGGTACGGTTTGAGGC'),
end_sequence=('BC90_rev', 'GCCTCAAACCGTACCCTCTACATC')),
Adapter('Barcode 91 (forward)',
start_sequence=('BC91', 'GGCTCCATAGGAACTCACGCTACT'),
end_sequence=('BC91_rev', 'AGTAGCGTGAGTTCCTATGGAGCC')),
Adapter('Barcode 92 (forward)',
start_sequence=('BC92', 'TTGTGAGTGGAAAGATACAGGACC'),
end_sequence=('BC92_rev', 'GGTCCTGTATCTTTCCACTCACAA')),
Adapter('Barcode 93 (forward)',
start_sequence=('BC93', 'AGTTTCCATCACTTCAGACTTGGG'),
end_sequence=('BC93_rev', 'CCCAAGTCTGAAGTGATGGAAACT')),
Adapter('Barcode 94 (forward)',
start_sequence=('BC94', 'GATTGTCCTCAAACTGCCACCTAC'),
end_sequence=('BC94_rev', 'GTAGGTGGCAGTTTGAGGACAATC')),
Adapter('Barcode 95 (forward)',
start_sequence=('BC95', 'CCTGTCTGGAAGAAGAATGGACTT'),
end_sequence=('BC95_rev', 'AAGTCCATTCTTCTTCCAGACAGG')),
Adapter('Barcode 96 (forward)',
start_sequence=('BC96', 'CTGAACGGTCATAGAGTCCACCAT'),
end_sequence=('BC96_rev', 'ATGGTGGACTCTATGACCGTTCAG'))]
def make_full_native_barcode_adapter(barcode_num):
barcode = [x for x in ADAPTERS if x.name == 'Barcode ' + str(barcode_num) + ' (reverse)'][0]
start_barcode_seq = barcode.start_sequence[1]
end_barcode_seq = barcode.end_sequence[1]
start_full_seq = 'AATGTACTTCGTTCAGTTACGTATTGCTAAGGTTAA' + start_barcode_seq + 'CAGCACCT'
end_full_seq = 'AGGTGCTG' + end_barcode_seq + 'TTAACCTTAGCAATACGTAACTGAACGAAGT'
return Adapter('Native barcoding ' + str(barcode_num) + ' (full sequence)',
start_sequence=('NB' + '%02d' % barcode_num + '_start', start_full_seq),
end_sequence=('NB' + '%02d' % barcode_num + '_end', end_full_seq))
def make_old_full_rapid_barcode_adapter(barcode_num): # applies to SQK-RBK001
barcode = [x for x in ADAPTERS if x.name == 'Barcode ' + str(barcode_num) + ' (forward)'][0]
start_barcode_seq = barcode.start_sequence[1]
start_full_seq = 'AATGTACTTCGTTCAGTTACG' + 'TATTGCT' + start_barcode_seq + \
'GTTTTCGCATTTATCGTGAAACGCTTTCGCGTTTTTCGTGCGCCGCTTCA'
return Adapter('Rapid barcoding ' + str(barcode_num) + ' (full sequence, old)',
start_sequence=('RB' + '%02d' % barcode_num + '_full', start_full_seq))
def make_new_full_rapid_barcode_adapter(barcode_num): # applies to SQK-RBK004
barcode = [x for x in ADAPTERS if x.name == 'Barcode ' + str(barcode_num) + ' (forward)'][0]
start_barcode_seq = barcode.start_sequence[1]
start_full_seq = 'AATGTACTTCGTTCAGTTACG' + 'GCTTGGGTGTTTAACC' + start_barcode_seq + \
'GTTTTCGCATTTATCGTGAAACGCTTTCGCGTTTTTCGTGCGCCGCTTCA'
return Adapter('Rapid barcoding ' + str(barcode_num) + ' (full sequence, new)',
start_sequence=('RB' + '%02d' % barcode_num + '_full', start_full_seq))