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replikation / poreCov

SARS-CoV-2 workflow for nanopore sequence data
https://case-group.github.io/
GNU General Public License v3.0
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Amplicon repair script only outputs repair primer IDs for V3 and V1200 #148

Closed hoelzer closed 2 years ago

hoelzer commented 3 years ago

I just noticed that, should be relatively easy to also provide potential "repair primers" for V4?

replikation commented 3 years ago

yep just add the line:

https://github.com/replikation/poreCov/blob/master/workflows/process/seqrs.nf

nothing fancy :D

hoelzer commented 3 years ago

Hah okay, easy thx for the hint ;)

hoelzer commented 3 years ago

Ah just wonder if there is an issue w/ your script because the input bed are a bit different:

(base) ➜  poreCov git:(V4_primers_out) ✗ head data/external_primer_schemes/nCoV-2019/V3/nCoV-2019.bed
MN908947.3  30  54  nCoV-2019_1_LEFT    nCoV-2019_1 +
MN908947.3  385 410 nCoV-2019_1_RIGHT   nCoV-2019_1 -
MN908947.3  320 342 nCoV-2019_2_LEFT    nCoV-2019_2 +
MN908947.3  704 726 nCoV-2019_2_RIGHT   nCoV-2019_2 -
MN908947.3  642 664 nCoV-2019_3_LEFT    nCoV-2019_1 +
MN908947.3  1004    1028    nCoV-2019_3_RIGHT   nCoV-2019_1 -
MN908947.3  943 965 nCoV-2019_4_LEFT    nCoV-2019_2 +
MN908947.3  1312    1337    nCoV-2019_4_RIGHT   nCoV-2019_2 -
MN908947.3  1242    1264    nCoV-2019_5_LEFT    nCoV-2019_1 +
MN908947.3  1623    1651    nCoV-2019_5_RIGHT   nCoV-2019_1 -
(base) ➜  poreCov git:(V4_primers_out) ✗ head data/external_primer_schemes/nCoV-2019/V4/nCoV-2019.primer.bed 
MN908947.3  25  50  SARS-CoV-2_1_LEFT   1   +   AACAAACCAACCAACTTTCGATCTC
MN908947.3  408 431 SARS-CoV-2_1_RIGHT  1   -   CTTCTACTAAGCCACAAGTGCCA
MN908947.3  324 344 SARS-CoV-2_2_LEFT   2   +   TTTACAGGTTCGCGACGTGC
MN908947.3  705 727 SARS-CoV-2_2_RIGHT  2   -   ATAAGGATCAGTGCCAAGCTCG
MN908947.3  644 666 SARS-CoV-2_3_LEFT   1   +   GTAATAAAGGAGCTGGTGGCCA
MN908947.3  1017    1044    SARS-CoV-2_3_RIGHT  1   -   GCCAATTTAATTTCAAAAGGTGTCTGC
MN908947.3  944 966 SARS-CoV-2_4_LEFT   2   +   GTGTATACTGCTGCCGTGAACA
MN908947.3  1337    1362    SARS-CoV-2_4_RIGHT  2   -   ACAACAGCATTTTGGGGTAAGTAAC
MN908947.3  1245    1266    SARS-CoV-2_5_LEFT   1   +   TGAAACTTCATGGCAGACGGG
MN908947.3  1623    1650    SARS-CoV-2_5_RIGHT  1   -   TTGATGTTGACTTTCTCTTTTTGGAGT

but this we can also test

replikation commented 3 years ago

as long as it is a correct bed file, it shouldn't be an issue. I use biorust to gather the bed file information. so i don't really parse anything out of it by e.g. columns or so.

we can discuss this further here: https://github.com/replikation/seqrs (code: https://github.com/replikation/seqrs/blob/main/src/main.rs)

hoelzer commented 2 years ago

seems to work fine, see #153 I do some more test and then merge