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added the latest midnight primers (V5.2.0_1200) #269

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merged 5 commits into from
Jul 23, 2024
Merged

added the latest midnight primers (V5.2.0_1200) #269

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27cff30
added the latest midnight primers (V5.2.0_1200)
MarieLataretu May 17, 2024
d679cf8
added V5.2.0_1200 for auto-read length filtering
MarieLataretu May 21, 2024
bb7e70d
updated log, readme and help
MarieLataretu May 22, 2024
8d3c6e0
added V5.2.0_1200 to seqrs
MarieLataretu May 22, 2024
078eedb
fixed path to primer bed file
MarieLataretu May 22, 2024
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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -206,7 +206,7 @@ Sample_2021,barcode01,good
* poreCov was coded with "easy to use" in mind, while staying flexible
* therefore we provide a few input types which adjusts the workflow automatically (see image below)
* fast5 raw data, fastq files (one sample per file), fastq_pass (the basecalling output) or fasta (supports multifastas)
* primer schemes for ARTIC can be V1, V2, V3(default), V4, V4.1 or V1200 (the 1200bp amplicon ones)
* primer schemes for ARTIC can be V1, V2, V3(default), V4, V4.1 (the 400bp amplicon ones), V1200 or V5.2.0_1200 (the 1200bp amplicon ones)

<p align="left">
<img src="data/figures/workflow.png" width="700" title="Workflow">
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1 change: 1 addition & 0 deletions data/external_primer_schemes/nCoV-2019/V5.2.0_1200/README.md
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https://github.com/quick-lab/SARS-CoV-2/blob/a716b8b5f5a1f31946ddf075e3ec60b09e09096d/1200/v5.2.0_1200/SARS-CoV-2_v5.2.0_1200.primer.bed
58 changes: 58 additions & 0 deletions data/external_primer_schemes/nCoV-2019/V5.2.0_1200/nCoV-2019.primer.bed
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MN908947.3 45 73 SARS-CoV-2_1200_1_LEFT 1 + ATCTCTTGTAGATCTGTTCTCTAAACGA
MN908947.3 1157 1185 SARS-CoV-2_1200_1_RIGHT 1 - GCAACTGGATAGACAGATCGAATTCTAC
MN908947.3 1073 1103 SARS-CoV-2_1200_2_LEFT 2 + GTCCAAATTTTGTATTTCCCTTAAATTCCA
MN908947.3 2185 2213 SARS-CoV-2_1200_2_RIGHT 2 - TAACAATTTCCCAACCGTCTCTAAGAAA
MN908947.3 2105 2135 SARS-CoV-2_1200_3_LEFT 1 + CTAACATCTTTGGCACTGTTTATGAAAAAC
MN908947.3 3226 3246 SARS-CoV-2_1200_3_RIGHT 1 - CTGCCGTCTTGTTGACCAAC
MN908947.3 3154 3176 SARS-CoV-2_1200_4_LEFT 2 + GCCACTTCTGCTGCTCTTCAAC
MN908947.3 4270 4294 SARS-CoV-2_1200_4_RIGHT 2 - CTTTGCCTCCTCTACAGTGTAACC
MN908947.3 4187 4211 SARS-CoV-2_1200_5_LEFT 1 + GCACTACTGAAATGCTAGCGAAAG
MN908947.3 5299 5327 SARS-CoV-2_1200_5_RIGHT 1 - ACTCTATTTGTTGGAGTGTTAACAATGC
MN908947.3 5198 5229 SARS-CoV-2_1200_6_LEFT 2 + GGTACATGTCAGCATTAAATCACACTAAAAA
MN908947.3 6329 6356 SARS-CoV-2_1200_6_RIGHT 2 - CTGACTTCAGTACATCAAACGAATTTG
MN908947.3 6250 6279 SARS-CoV-2_1200_7_LEFT 1 + AATGCAACTAATAAAGCCACGTATAAACC
MN908947.3 7357 7390 SARS-CoV-2_1200_7_RIGHT 1 - GGCCATTTGTACAAGATTAATTATTAACCACAT
MN908947.3 7282 7306 SARS-CoV-2_1200_8_LEFT 2 + GTACTTGGATTGGCTGCAATCATG
MN908947.3 8393 8423 SARS-CoV-2_1200_8_RIGHT 2 - ACATGAAATCTTTAACGTTCCATATCAAAG
MN908947.3 8320 8343 SARS-CoV-2_1200_9_LEFT 1 + CGTGACCTTGGTGCTTGTATTGA
MN908947.3 9430 9460 SARS-CoV-2_1200_9_RIGHT 1 - CATAAAATAGTAGGCAAGGCATGTTACTAC
MN908947.3 9347 9380 SARS-CoV-2_1200_10_LEFT 2 + CTAATATGTTTACACCACTAATTCAACCTATTG
MN908947.3 10461 10488 SARS-CoV-2_1200_10_RIGHT 2 - CATGAACCATTAAGGAATGAACCCTTA
MN908947.3 10381 10411 SARS-CoV-2_1200_11_LEFT 1 + CAGACTTTTTCAGTGTTAGCTTGTTACAAT
MN908947.3 11474 11507 SARS-CoV-2_1200_11_RIGHT 1 - CTACACCTGAGTAGTTAGAAGTAACAGAGATTA
MN908947.3 11390 11417 SARS-CoV-2_1200_12_LEFT 2 + GGACACTTATGAATGTCTTGACACTCG
MN908947.3 12498 12530 SARS-CoV-2_1200_12_RIGHT 2 - ATGTTGTACCATCACACGTATTTTTATATGTG
MN908947.3 12419 12444 SARS-CoV-2_1200_13_LEFT 1 + CAAGAGATGGTTGTGTTCCCTTGAA
MN908947.3 13530 13559 SARS-CoV-2_1200_13_RIGHT 1 - TCATTGTAGATGTCAAAAGCCCTGTATAC
MN908947.3 13458 13480 SARS-CoV-2_1200_14_LEFT 2 + GTTTTTAAACGGGTTTGCGGTG
MN908947.3 14579 14599 SARS-CoV-2_1200_14_RIGHT 2 - GATTACCAGAAGCAGCGTGC
MN908947.3 14491 14524 SARS-CoV-2_1200_15_LEFT 1 + TAGGTGTTGTACATAATCAGGATGTAAACTTAC
MN908947.3 15601 15631 SARS-CoV-2_1200_15_RIGHT 1 - GACACTCATAAAGTCTGTGTTGTAAATTGC
MN908947.3 15531 15551 SARS-CoV-2_1200_16_LEFT 2 + CAAGCTGTCACGGCCAATGT
MN908947.3 16646 16671 SARS-CoV-2_1200_16_RIGHT 2 - AAATGTCTCCTCAGTAGCTTTGAGC
MN908947.3 16571 16596 SARS-CoV-2_1200_17_LEFT 1 + TGACTGGACAAATGCTGGTGATTAC
MN908947.3 17686 17711 SARS-CoV-2_1200_17_RIGHT 1 - TGTGGCCTGTTAATTGCAGATGAAA
MN908947.3 17595 17627 SARS-CoV-2_1200_18_LEFT 2 + GCTTTGGTTTATGATAATAAGCTTAAAGCACA
MN908947.3 18712 18737 SARS-CoV-2_1200_18_RIGHT 2 - AATCCAATAGAATGATGCCAACAGG
MN908947.3 18636 18658 SARS-CoV-2_1200_19_LEFT 1 + AAAATAGGACCTGAGCGCACCT
MN908947.3 19762 19790 SARS-CoV-2_1200_19_RIGHT 1 - AGCTCAAATGCTACATTAACAGGTAATG
MN908947.3 19679 19712 SARS-CoV-2_1200_20_LEFT 2 + TGAAGTACCAGTTTCTATCATTAATAACACTGT
MN908947.3 20787 20819 SARS-CoV-2_1200_20_RIGHT 2 - AAATATTGACACAGTTGAGTATATTTTGCGAC
MN908947.3 20682 20711 SARS-CoV-2_1200_21_LEFT 1 + GTTGCTATGCCTAATCTTTACAAAATGCA
MN908947.3 21801 21828 SARS-CoV-2_1200_21_RIGHT 1 - CCATCATTAAATGGTAGGACAGGGTTA
MN908947.3 21695 21723 SARS-CoV-2_1200_22_LEFT 2 + CCTCAGTTTTACATTCAACTCAGGACTT
MN908947.3 22825 22858 SARS-CoV-2_1200_22_RIGHT 2 - GCAGCCTGTAAAATCATCTGGTAATTTATAATT
MN908947.3 22742 22774 SARS-CoV-2_1200_23_LEFT 1 + ATGTCTATGCAGATTCATTTGTAATTAGAGGT
MN908947.3 23868 23895 SARS-CoV-2_1200_23_RIGHT 1 - GTGTTTTTGTCTTGTTCAACAGCTATT
MN908947.3 23784 23811 SARS-CoV-2_1200_24_LEFT 2 + CATTTGTGGTGATTCAACTGAATGCAG
MN908947.3 24875 24905 SARS-CoV-2_1200_24_RIGHT 2 - TGATTTGTGGTTCATAAAAATTCCTTTGTG
MN908947.3 24797 24822 SARS-CoV-2_1200_25_LEFT 1 + CTGCCATTTGTCATGATGGAAAAGC
MN908947.3 25911 25937 SARS-CoV-2_1200_25_RIGHT 1 - TGTTCAGAAATAGGACTTGTTGTGCC
MN908947.3 25784 25809 SARS-CoV-2_1200_26_LEFT 2 + GAAATGCCGTTCCAAAAACCCATTA
MN908947.3 26899 26924 SARS-CoV-2_1200_26_RIGHT 2 - TAGAAGCGGTCTGGTCAGAATAGTG
MN908947.3 26818 26840 SARS-CoV-2_1200_27_LEFT 1 + TTTCAGACTGTTTGCGCGTACG
MN908947.3 27934 27962 SARS-CoV-2_1200_27_RIGHT 1 - CTGTAAACTACATTCTTGGTGAAATGCA
MN908947.3 27832 27860 SARS-CoV-2_1200_28_LEFT 2 + TATCTTTTGGTTCTCACTTGAACTGCAA
MN908947.3 28945 28969 SARS-CoV-2_1200_28_RIGHT 2 - GCTCTCAAGCTGGTTCAATCTGTC
MN908947.3 28702 28723 SARS-CoV-2_1200_29_LEFT 1 + GATCACATTGGCACCCGCAAT
MN908947.3 29779 29802 SARS-CoV-2_1200_29_RIGHT 1 - GGCTCTTCCATATAGGCAGCTCT
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