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  • Generation of 192 barcode sequences that are furthest apart

    Dear all,

    we are working on implementing MARS-seq in our lab and for this purpose we would need to generate unique barcodes (6 bases barcode). We would like to scramble the X's (see below) to achieve 192 combinations but where the barcodes are the furthest apart from each other.

    CTTCCGATCTXXXXXX

    Do you know a good way to do it? Maybe such a script exists already?

    Thanks a lot!

    Best,

    Kevin

  • #2
    I think these are all 2 steps from each other.. to get to 3 steps it would need a 7mer. This isn't an optimal hamming solution, but would work.
    1 CTCATT
    2 GTAAGT
    3 TGCGGA
    4 GAGATG
    5 ATGCTG
    6 CTGAGT
    7 CTCTAG
    8 TTAGTG
    9 GAATTC
    10 GCACCG
    11 ATCTTA
    12 AGTAGG
    13 TGATTT
    14 GTTATT
    15 AGTGTT
    16 GCTTTA
    17 CAGTAA
    18 GTTGAT
    19 GCATCC
    20 TTATAT
    21 TCCTCT
    22 TAGGTC
    23 GTTTAA
    24 GGCGAA
    25 AGCACT
    26 GGTAAT
    27 GCTGGT
    28 TAGAAA
    29 CCAATC
    30 TAGGCT
    31 CTTACG
    32 AGATAT
    33 ACCACA
    34 ATTTTT
    35 AGCTGA
    36 AAAAGG
    37 TACTTT
    38 CCTGTG
    39 TGCTTG
    40 ACACCC
    41 TTGTGG
    42 TCATGG
    43 TGAACA
    44 AGAGTC
    45 CGACCT
    46 CAACGT
    47 GCTCCT
    48 ACGAGC
    49 ACTACT
    50 GCCTGC
    51 ACGCTC
    52 ATCGGA
    53 ATGGGC
    54 CAACCC
    55 CCGATG
    56 AAAGTG
    57 CGAAGC
    58 AACTCC
    59 CCGCTT
    60 AATACC
    61 AGAAGA
    62 TGGTAC
    63 CTGGCA
    64 TATGGG
    65 GACCTC
    66 CAATCA
    67 CTTGCC
    68 CGATCC
    69 TCTCTC
    70 ATCTCG
    71 AATATT
    72 CTAAAA
    73 GAAGAC
    74 CGGCTA
    75 CGAGTA
    76 TCTTAA
    77 GTATTT
    78 AAGGAT
    79 TACCGA
    80 GGAGAT
    81 GCCATC
    82 AGGATT
    83 TCAAAC
    84 ACTTGC
    85 TACTCG
    86 GCTCTG
    87 GGGGCC
    88 AGGACG
    89 TAAGTA
    90 GACCCA
    91 GCCTCA
    92 TAAAAG
    93 CGTTCT
    94 TCCGTT
    95 TCTTTG
    96 TTCGAG
    97 CGCGTG
    98 TCCCAG
    99 CTAGCT
    100 CAATAG
    101 TTGATA
    102 AGCCAC
    103 GCCTAG
    104 CATAAT
    105 CGACGG
    106 TACACA
    107 GAGGTA
    108 AACGGG
    109 AGAAAG
    110 GCGGCA
    111 TGTCTT
    112 ATCTAC
    113 AAGATA
    114 CTTTTC
    115 CGAATG
    116 GAGGGT
    117 GCCAAT
    118 GTTGCA
    119 CTTCTT
    120 ACATAC
    121 GCGGAT
    122 AAGCCA
    123 TATCCA
    124 AGCCGG
    125 CACGCC
    126 CTCTGT
    127 TACCTG
    128 TCGGAA
    129 ATCCGT
    130 GTTTGC
    131 TTTCAC
    132 AATTAC
    133 CCGACA
    134 TCAACG
    135 CCTAGG
    136 CGTTTG
    137 AGTATC
    138 ATATGG
    139 CAGCAT
    140 AAACCG
    141 GATGTC
    142 GCCGTG
    143 TTGGAC
    144 GAACAG
    145 AGATCG
    146 TACGAA
    147 CGAGAC
    148 GCGTCG
    149 GATCCC
    150 CACGAT
    151 GATAGC
    152 TGGCCA
    153 TGCCGC
    154 GGAGGA
    155 TTTAGT
    156 TCTGGA
    157 TAATAC
    158 CATCTG
    159 GGACGT
    160 AGTAAA
    161 GGGCAG
    162 CCAACT
    163 CCCGGT
    164 CGGGCT
    165 TCATTA
    166 GCACAC
    167 TGGGAG
    168 CGTGGG
    169 CATGAG
    170 AGCGCG
    171 GTGTAG
    172 CTGGTT
    173 AAGGCG
    174 TGGCTG
    175 CCGCGA
    176 TTCGCA
    177 AAAAAC
    178 GAGCAA
    179 CTAGGG
    180 AGTTCA
    181 TAAATC
    182 GACTTG
    183 GTACAT
    184 AATTGT
    185 TGTTGG
    186 TCCATG
    187 GGTTTT
    188 GATCTT
    189 TGACAT
    190 CACAAC
    191 GTGAGC
    192 TCGCCC
    193 CCCTTG
    194 CGCCCG
    195 GGTGAG
    196 TCTGCG
    197 AGGGGA
    198 CTCCCC
    199 GCAGAG
    200 GGGCGC
    201 GATGAA
    202 CGTAGA
    203 CCCGAA
    204 TTATCG
    205 ATTATA
    206 ATCGTC
    207 CGCTGG
    208 TTCGGT
    209 TGCAAC
    210 TCCCGT
    211 GGAGCG
    212 TGTGTA
    213 CCCACG
    214 GAGAAT
    215 ATTGCG
    216 ATACAA
    217 TTCAAT
    218 TGTGGC
    219 ACGTCT
    220 AAGCAG
    221 ATCGAT
    222 ACCTGT
    223 CCTTCC
    224 TCCCTA
    225 CCTCAC
    226 TTAACT
    227 CCGTAT
    228 CCTCGT
    229 GCTTGG
    230 ATAAAT
    231 TCCTTC
    232 ACGGCC
    233 ACCGAG
    234 TAATGT
    235 GACCGG
    236 ATGCAC
    237 CCTTGA
    238 CCATCG
    239 AGAGAA
    240 GTCTGG
    241 CAGTCG
    242 TTTGTT
    243 ACGCAT
    244 CGTCCC
    245 AACCCT
    246 CTGCTC
    247 TTAGGC
    248 TGAGCT
    249 GGCATG
    250 CCCCGC
    251 GTGACA
    252 ACACGT
    253 CTGTAC
    254 GGGTCA
    255 GATGCT
    256 TGATAA
    257 TTCCAA
    258 GTTCTC
    259 TTAAGA
    260 TTCAGC
    261 TCACCT
    262 GAATGG
    263 TGTGAT
    264 ATAACA
    265 TGGACT
    266 GTCATA
    267 GCGTAA
    268 CTGTTG
    269 TGCATA
    270 CCCGTC
    271 AACGAC
    272 AGGTGC
    273 GACACC
    274 AAAACT
    275 TGAAGT
    276 CAGACT
    277 GTACCC
    278 CTGGAG
    279 CTACTA
    280 GGCGCT
    281 CGCACA
    282 TGGATC
    283 GACAAA
    284 ATGGCT
    285 CGCCGA
    286 GATTCA
    287 GCGAGT
    288 ATTAGC
    289 AGTGAC
    290 GTGCCG
    291 TTGCGT
    292 AGCTTT
    293 ACTATG
    294 TTGTTC
    295 TCTCAT
    296 GGCCCC
    297 GTGCTT
    298 AAATGA
    299 TGATGC
    300 CAAGCG
    301 TGCAGG
    302 ATCAAG
    303 TCGATT
    304 TGTCCG
    305 CTTGTA
    306 GTCCGA
    307 GAACTA
    308 TATCGC
    309 TAGTCA
    310 CAGGGG
    311 AGACTT
    312 TGGTTA
    313 TTGGCG
    314 GTCCCT
    315 CAAGAA
    316 CACCTT
    317 CTCCGG
    318 GCAATA
    319 GTAATG
    320 GCGGTC
    321 AGCGGT
    322 ACGTAG
    323 ACAGTA
    324 AGACGC
    325 ACTCAG
    326 TCGTGC
    327 CGGAAA
    328 CGTTAA
    329 CTGCCT
    330 CAAGTC
    331 CAGGAC
    332 ATTCGG
    333 GGCTAT
    334 CGACAA
    335 CCAGCA
    336 GGCTTA
    337 ACAGCT
    338 GAGTCC
    339 GACGTT
    340 CCGTGG
    341 GGAACC
    342 ATTCCA
    343 ACGGGG
    344 CGGCAC
    345 GGGATA
    346 AACAGC
    347 CCTCCG
    348 GTTTTG
    349 TTCCTC
    350 TATATG
    351 ACTTCG
    352 CACATG
    353 GACGAG
    354 ATACTC
    355 AGGCGT
    356 TAACTT
    357 TTTAAA
    358 ACGCCG
    359 TATGAC
    360 TCCGGG
    361 AATCAT
    362 AGGCCC
    363 GGGTTC
    364 CATTTT
    365 GCCGAC
    366 TTCTCC
    367 AGGTTG
    368 TGTTCC
    369 TAGCGG
    370 TGACTA
    371 TGCTCA
    372 AATCGA
    373 AACTAG
    374 GTCCAG
    375 CGGGTC
    376 GGTTGA
    377 CCGCAG
    378 CCTAAA
    379 GTTAAC
    380 TGGTGT
    381 GATTAG
    382 GGTTAC
    383 CTCCAT
    384 AGCCTA
    385 GTCGGC
    386 ACAGGC
    387 AATTTA
    388 AAGTGG
    389 GATATA
    390 AAAGCC
    391 GGGGTT
    392 GTTGGG
    393 TGGTCG
    394 CCTATT
    395 ACATCA
    396 CTGCAA
    397 TTGTAA
    398 TATAGA
    399 TTACGG
    400 GGCGTC
    401 GCTACC
    402 ATGATC
    403 GGACTG
    404 CCATAA
    405 AACGTA
    406 TCTACA
    407 AGGCAA
    408 CTTTGG
    409 ACTGAA
    410 GGGCCT
    411 TTGAAG
    412 CAGTGC
    413 CGCCTC
    414 GCTTAT
    415 GTAGTC
    416 CGGAGG
    417 GAAGCA
    418 AGAGGG
    419 GGAATT
    420 GTGGGA
    421 AACACG
    422 AGTCCT
    423 CGGACC
    424 CATGGA
    425 TCTAAG
    426 TCGAGA
    427 GTATAC
    428 CGTCAG
    429 GAAACG
    430 TAGCAC
    431 AATAAG
    432 CACTTC
    433 CTTCGC
    434 CTTTCA
    435 AGATTA
    436 CCCAGA
    437 CTACAG
    438 GCCTTT
    439 TCACGC
    440 TCCTGA
    441 TTTTTA
    442 CGGTGA
    443 CGAAAT
    444 ACTAGA
    445 ATACCT
    446 AACAAT
    447 GACTGA
    448 GGTACG
    449 GACCAT
    450 CGCAGT
    451 TTTTAG
    452 TGTCGA
    453 GTATGA
    454 GGCTCG
    455 TCCGCC
    456 CCTGGC
    457 GAATAT
    458 TTTACC
    459 TAAGAT
    460 CCCTAC
    461 TATCAG
    462 ACAAAA
    463 ATTTCC
    464 ATGAGG
    465 ACATTT
    466 TATTAT
    467 TGCCCT
    468 GTCTTC
    469 TTCACG
    470 GGATCT
    471 ATGGAA
    472 AATCTC
    473 ATAGGT
    474 TAATTG
    475 TAGGGA
    476 GACAGT
    477 CGTAAC
    478 GGACCA
    479 TACCCC
    480 ACCCTT
    481 CATACA
    482 GCGAAG
    483 CCTCTA
    484 GTGGTG
    485 CCGTTC
    486 CGCAAG
    487 GGGAAC
    488 TTTTCT
    489 ATGCGA
    490 GGGTGG
    491 AAGCTT
    492 GCTCAA
    493 CATCCT
    494 ACCAGG
    495 GTGTGT
    496 CACCAA
    497 ATCACC
    498 TAGCTA
    499 ACCCAA
    500 TCGGGT
    501 ACTGTC
    502 GGAAAA
    503 CGTTGC
    504 CCTTAG
    505 GACTAC
    506 CAAAGA
    507 TATACT
    508 TTACCA
    509 GAACCT
    510 ACTAAC
    511 CAAATT
    512 TCCAAA
    513 GCATTG
    514 ACGGTT
    515 ATGTCA
    516 GCGCTA
    517 ACGTTA
    518 CGAGGT
    519 AGTTAG
    520 GGCCTT
    521 CACTCT
    522 TCGGTG
    523 ATTTGA
    524 GTGTTA
    525 AAGCGC
    526 CAGATC
    527 CCTGAT
    528 GCACTT
    529 GCTCGC
    530 GCATGT
    531 CCATGC
    532 CCGAAC
    533 CTCGCG
    534 CTAACC
    535 CGGTAG
    536 TACTGC
    537 CTTTAT
    538 CCGGCG
    539 TAACAA
    540 GCAAGC
    541 TCTTGT
    542 GGATAG
    543 CCAAAG
    544 AAGAGT
    545 AATGGC
    546 ACACTG
    547 CAGAAG
    548 AAGTTC
    549 GTAGAA
    550 GCCGGA
    551 GGCAGA
    552 GTTCGT
    553 TAGACG
    554 CTTGGT
    555 ATAGAC
    556 GCACGA
    557 CGGTTT
    558 TCTCGG
    559 GAACGC
    560 GGCGGG
    561 CCAGTT
    562 GAGTTT
    563 GCGCGG
    564 GAGAGA
    565 TGACCC
    566 CGTGCA
    567 CCGGTA
    568 ATGTAT
    569 GTTAGA
    570 AGTCTG
    571 GGAAGG
    572 CCCCCA
    573 TATTTC
    574 CTCGAC
    575 TTTCTG
    576 TAGTAG
    577 AATGCA
    578 GGTCGG
    579 TCTAGC
    580 CCACAT
    581 GGTCTA
    582 TCAGTC
    583 CGCGGC
    Providing nextRAD genotyping and PacBio sequencing services. http://snpsaurus.com

    Comment


    • #3
      I haven't used it for 6bp tags, but I've found the following helpful for generating tags and validating tag edit distances:
      edit distance sequence tags and helpers. Contribute to faircloth-lab/edittag development by creating an account on GitHub.


      Corresponding publication:
      Faircloth BC, Glenn TC. 2012. Not all sequence tags are created equal: Designing and validating sequence identification tags robust to indels. PLoS ONE 7(8): e42543.

      Comment


      • #4
        Thanks a lot, guys. Very helpful!

        Comment

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