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UPHL-BioNGS / Cecret

Reference-based consensus creation
MIT License
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mpx primer additions #121

Closed tives82 closed 1 year ago

tives82 commented 1 year ago

Erin, I thought I'd just do a PR to add the mpx primer profile to save you a little time rather than sending you the files by other means but please change anything I've done however you'd like. I've selected to allow edits.

erinyoung commented 1 year ago

I think this looks okay, but I can't change the default MPX to ON568298.1

erinyoung commented 1 year ago

I think we need to adjust the primer bedfile to NC_063383.1 coordinates

fanninpm commented 1 year ago

@erinyoung Do you instead want the primers from this protocol by Chen et al?

erinyoung commented 1 year ago

@fanninpm the primalseq primers would be good to add, too.

primalseq uses MT903345 for their reference.

MT903345    356 378 MPXV_1_LEFT 1   +
MT903345    2395    2417    MPXV_1_RIGHT    1   -
MT903345    1439    1461    MPXV_2_LEFT 2   +
MT903345    3353    3375    MPXV_2_RIGHT    2   -
MT903345    2606    2628    MPXV_3_LEFT 1   +
MT903345    4593    4615    MPXV_3_RIGHT    1   -
MT903345    3990    4012    MPXV_4_LEFT 2   +
MT903345    5584    5607    MPXV_4_RIGHT    2   -
MT903345    4991    5013    MPXV_5_LEFT 1   +
MT903345    7027    7049    MPXV_5_RIGHT    1   -
MT903345    6134    6156    MPXV_6_LEFT 2   +
MT903345    8202    8224    MPXV_6_RIGHT    2   -
MT903345    7417    7439    MPXV_7_LEFT 1   +
MT903345    9405    9427    MPXV_7_RIGHT    1   -
MT903345    8858    8880    MPXV_8_LEFT 2   +
MT903345    10646   10668   MPXV_8_RIGHT    2   -
MT903345    9767    9789    MPXV_9_LEFT 1   +
MT903345    11731   11753   MPXV_9_RIGHT    1   -
MT903345    10729   10751   MPXV_10_LEFT    2   +
MT903345    12880   12902   MPXV_10_RIGHT   2   -
MT903345    12290   12312   MPXV_11_LEFT    1   +
MT903345    14020   14042   MPXV_11_RIGHT   1   -
MT903345    13079   13101   MPXV_12_LEFT    2   +
MT903345    15347   15369   MPXV_12_RIGHT   2   -
MT903345    14663   14685   MPXV_13_LEFT    1   +
MT903345    16733   16755   MPXV_13_RIGHT   1   -
MT903345    15866   15888   MPXV_14_LEFT    2   +
MT903345    18116   18138   MPXV_14_RIGHT   2   -
MT903345    17282   17304   MPXV_15_LEFT    1   +
MT903345    19262   19284   MPXV_15_RIGHT   1   -
MT903345    18294   18316   MPXV_16_LEFT    2   +