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Drosten PCR Essay
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| #!/bin/bash | |
| function check() { | |
| echo "------------------------------------------------------------" | |
| echo "$1" | |
| seqkit amplicon -F "$1" "$2" | |
| } | |
| echo "------------------------------------------------------------" | |
| echo "MN908947.1" | |
| check "GTGARATGGTCATGTGTGGCGG" "out/MN908947.1.fasta" | |
| check "CAGGTGGAACCTCATCAGGAGATGC" "out/MN908947.1.fasta" | |
| check "CCAGGTGGWACRTCATCMGGTGATGC" "out/MN908947.1.fasta" | |
| check "CARATGTTAAASACACTATTAGCATA" "out/MN908947.1.fasta" | |
| check "ACAGGTACGTTAATAGTTAATAGCGT" "out/MN908947.1.fasta" | |
| check "ACACTAGCCATCCTTACTGCGCTTCG" "out/MN908947.1.fasta" | |
| check "ATATTGCAGCAGTACGCACACA" "out/MN908947.1.fasta" | |
| check "CACATTGGCACCCGCAATC" "out/MN908947.1.fasta" | |
| check "ACTTCCTCAAGGAACAACATTGCCA" "out/MN908947.1.fasta" | |
| check "GAGGAACGAGAAGAGGCTTG" "out/MN908947.1.fasta" | |
| echo "------------------------------------------------------------" | |
| echo "MN908947.2" | |
| check "GTGARATGGTCATGTGTGGCGG" "out/MN908947.2.fasta" | |
| check "CAGGTGGAACCTCATCAGGAGATGC" "out/MN908947.2.fasta" | |
| check "CCAGGTGGWACRTCATCMGGTGATGC" "out/MN908947.2.fasta" | |
| check "CARATGTTAAASACACTATTAGCATA" "out/MN908947.2.fasta" | |
| check "ACAGGTACGTTAATAGTTAATAGCGT" "out/MN908947.2.fasta" | |
| check "ACACTAGCCATCCTTACTGCGCTTCG" "out/MN908947.2.fasta" | |
| check "ATATTGCAGCAGTACGCACACA" "out/MN908947.2.fasta" | |
| check "CACATTGGCACCCGCAATC" "out/MN908947.2.fasta" | |
| check "ACTTCCTCAAGGAACAACATTGCCA" "out/MN908947.2.fasta" | |
| check "GAGGAACGAGAAGAGGCTTG" "out/MN908947.2.fasta" | |
| echo "------------------------------------------------------------" | |
| echo "MN908947.3" | |
| check "GTGARATGGTCATGTGTGGCGG" "out/MN908947.3.fasta" | |
| check "CAGGTGGAACCTCATCAGGAGATGC" "out/MN908947.3.fasta" | |
| check "CCAGGTGGWACRTCATCMGGTGATGC" "out/MN908947.3.fasta" | |
| check "CARATGTTAAASACACTATTAGCATA" "out/MN908947.3.fasta" | |
| check "ACAGGTACGTTAATAGTTAATAGCGT" "out/MN908947.3.fasta" | |
| check "ACACTAGCCATCCTTACTGCGCTTCG" "out/MN908947.3.fasta" | |
| check "ATATTGCAGCAGTACGCACACA" "out/MN908947.3.fasta" | |
| check "CACATTGGCACCCGCAATC" "out/MN908947.3.fasta" | |
| check "ACTTCCTCAAGGAACAACATTGCCA" "out/MN908947.3.fasta" | |
| check "GAGGAACGAGAAGAGGCTTG" "out/MN908947.3.fasta" | |
| echo "------------------------------------------------------------" |
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