diff --git a/config/rsvb.yaml b/config/rsvb.yaml new file mode 100644 index 00000000..35a77ed5 --- /dev/null +++ b/config/rsvb.yaml @@ -0,0 +1,27 @@ +# config file for Human respiratory syncytial virus B +# config file is used to process Illumina RSV samples + +general: + virus_base_config: "" + preprocessor: "prinseq" + aligner: "bwa" + primers_trimmer: "samtools" + +input: + datadir: "samples/" + samples_file: "samples.tsv" + read_length: 251 + primers_bedfile: "{VPIPE_BASEDIR}/../resources/rsvb/RSVB_primers_400_V2.1.bed" + inserts_bedfile: "{VPIPE_BASEDIR}/../resources/rsvb/RSVB_inserts_400_V2.1.bed" + reference: "{VPIPE_BASEDIR}/../resources/rsvb/MT107528.1.fasta" + +output: + datadir: "results" + trim_primers: true + snv: false + local: false + global: false +snv: + consensus: false +lofreq: + consensus: false diff --git a/resources/rsvb/MT107528.1.fasta b/resources/rsvb/MT107528.1.fasta new file mode 100644 index 00000000..e3a25a29 --- /dev/null +++ b/resources/rsvb/MT107528.1.fasta @@ -0,0 +1,221 @@ +>MT107528.1 Human respiratory syncytial virus B isolate HRSV/B/Bern/2019, complete genome +TGACGAAACGGAGTCTAGACTCCGTCACGCGAAAAAATGCGTACTACAAACTTGCACACTCGAAAAAAAT +GGGGCAAATAAGAATTTGATAAGTGCTATTTAAGTCTAACCTTTTTAATCAGAAATGGGGTGCAATTCAC +TGAGCATGATAAAGGTTAGATTACAAAATTTGTTTGATAATGACGAAGTAGCATTGTTAAAAATAACATG +TTATACTGACAAATTAATTCTTCTGACTAATGCATTAGCCAAAGCAACAATACATACAATTAAATTAAAC +GGCATAGTTTTTATACATGTTATAACAAGCAGTGAAGTGTGCCCTGATAACAATATTGTAGTGAAATCTA +ACTTTACAACAATGCCAATATTACAAAATGGAGGATACATATGGGAATTGATTGAATTGACACACTGCTC +TCAATTAAATGGTCTAATAGATGATAATTGTGAAATCAAATTTTCTAAAAGACTAAGTGACTCAGTAATG +ACTGATTATATGAATCAAATATCTGATTTACTTGGGCTTGATCTCCATTCATGAATTATGTTTAGTCTAA +TTCAATAGACATGTGTTTATTACCATTTTAGTTAATATAAAACCTCATCAAAGGGAGATGGGGCAAATAA +ACTCACCCAATCAATCAAACCATGAGCACTACAAACGACAACACCACCATGCAAAGATTGATGATCACAG +ACATGAGACCCCTGTCGATGGATTCAATAATAACATCTCTCACCAAAGAAATCATCACACACAAATTCAT +ATACTTGATAAACAATGAATGTATTGTAAGAAAACTCGATGAAAGACAAGCTACATTTACATTCCTAGTC +AATTATGAGATGAAGCTATTGCACAAAGTAGGGAGTACCAAATACAAGAAATACACCGAATATAATACAA +AATATGGCACATTCCCTATGCCTATATTTATCAATCATGGCGGGTTTCTAGAATGTATTGGCATTAAGCC +TACAAAACATACTCCTATAATATACAAATATGACCTCAACCCGTAACTTCCAACAAAAAAACCAACTCAT +CCAAACCAAGCCATTCTCCAAACAACAATGCTCAACAGTTAAGAAGGAGCTAATCCATTTTAGTAATTAA +AAATAAGGGTGAAACCAGTAACATAAATTGGGGCAAATACAAAGATGGCTCTTAGCAAAGTCAAGTTGAA +TGATACATTAAATAAGGATCAGCTGCTGTCATCCAGCAAATACACTATTCAACGTAGTACAGGAGATAAT +ATTGACACTCCCAATTATGATGTGCAAAAACACCTAAACAAACTATGTGGTATGCTATTAATCACTGAAG +ATGCAAATCATAAATTCACAGGATTAATAGGTATGCTATATGCTATGTCCAGATTAGGAAGGGAAGACAC +TATAAAGATACTTAAAGATGCTGGATATCATGTTAAAGCTAATGGAGTAGATATAACAACATATCGTCAA +GATATAAATGGAAAGGAAATGAAATTCGAAGTATTAACATTATCAAGCTTGACATCAGAAATACAAGTCA +ATATTGAGATAGAATCTAGAAAGTCCTACAAAAAAATGCTAAAAGAGATGGGAGAAGTGGCTCCAGAATA +TAGGCATGATTCTCCAGACTGTGGGATGATAATACTGTGTATAGCTGCCCTTGTAATAACCAAATTAGCA +GCAGGAGATAGATCAGGTCTTACAGCAGTAATTAGGAGGGCAAACAATGTCTTAAAAAACGAAATAAAAC +GCTACAAGGGCCTAATACCAAAAGACATAGCCAACAGTTTTTATGAAGTGTTTGAAAAATACCCTCATCT +TATAGATGTTTTTGTGCACTTTGGCATAGCACAATCATCCACAAGAGGGGGCAGTAGAGTTGAAGGAATC +TTTGCAGGATTGTTTATGAATGCCTATGGTTCAGGACAAGTAATGCTAAGATGGGGAGTTTTAGCCAAAT +CTGTAAAAAATATCATGCTAGGACATGCTAGTGTCCAAGCAGAAATGGAGCAAGTTGTGGAAGTCTATGA +GTATGCACAGAAGTTGGGAGGAGAAGCTGGTTTCTACCATATATTGAACAATCCAAAAGCATCATTGCTG +TCATTAACTCAATTTCCTAACTTCTCAAGTGTGGTCCTAGGCAATGCAGCAGGTCTAGGCATAATGGGAG +AGTATAGAGGTACACCAAGAAACCAAGATCTCTATGATGCAGCCAAAGCATATGCAGAGCAACTCAAAGA +AAATGGAGTAATAAACTACAGTGTATTAGACTTAACAACAGAAGAATTGGAAGCCATAAAGCATCAACTC +AACCCCAAAGAAGATGACGTAGAGCTTTAAGTTAACAAAAAATACGGGGCAAATAAGTCAACATGGAGAA +GTTTGCACCTGAATTTCATGGAGAAGACGCAAATAACAAAGCTACCAAATTCCTAGAATCAATAAAAGGC +AAGTTCGCATCATCCAAAGATCCTAAGAAGAAAGATAGCATAATATCTGTCAACTCAATAGACATAGAAG +TCACTAAAGAGAGCCCGATAACATCTGGCACCAACATTATCAATCCAACAAGTGAAGCCGACAGTACCCC +AGAAACTAAAGCCAACTACCCAAGAAAACCTCTAGTAAGCTTCAAAGAAGATCTCACCCCAAGTGATAAC +CCTTTCTCTAAGTTGTACAAAGAAACCATAGAAACATTTGATAACAATGAAGAAGAATCTAGCTACTCAT +ATGAGGAGATCAATGACCAAACAAATGACAACATTACAGCAAGACTAGATAGAATTGATGAAAAATTAAG +TGAAATATTAGGAATGCTCCATACATTAGTAGTTGCAAGTGCAGGACCTACTTCGGCTCGTGACGGAATA +AGAGATGCTATGGTTGGTCTAAGAGAAGAAATGATAGAAAAAATAAGAGCAGAAGCATTAATGACCAATG +ATAGGTTAGAGGCCATGGCAAGACTTAGGAATGAGGAAAGTGAAAAAATGGCAAAAGACACCTCAGATGA +AGTGTCTCTCAATCCAACCTCTAAAAAATTGAGTGACTTGTTGGAAGACAACGATAGCGACAATGATCTA +TCACTTGATGATTTTTGATCAGTGATCAACTCACTCAGCAATCAACAACATCAATAAAACAGACACCAAT +CCATTGAATCAATTGCCAGACTGAAAAAACAAACATCCATCAGCAGAACCACCAACCAATCAATCAACCA +ATTGATCAATCAGCACCCTGACAAAATTAACAATATAGTAACAAAAAAAGAACAAGATGGGGCAAATATG +GAAACATACGTGAACAAGCTTCACGAAGGCTCCACATACACAGCAGCTGTCCAGTACAATGTTCTAGAAA +AAGATGATGATCCCGCATCACTAACAATATGGGTGCCTATGTTCCAGTCATCTGTGCCAGCAGACTTGCT +CATAAAAGAACTTGCAAGCATCAACATACTAGTAAAGCAGATCTCTACGCCCAAAGGACCTTCACTACGA +GTCACGATCAACTCAAGAAGTGCTGTGCTGGCTCAAATGCCTAGTAATTTCACCATAAGTGCAAATGTAT +CATTAGATGAAAGAAGCAAATTAGCATATGATGTAACTACACCTTGTGAAATCAAAGCATGCAGTTTAAC +ATGCTTAAAAGTAAAAAGTATGTTAACTACAGTCAAAGATCTAACCATGAAGACATTCAACCCCACTCAT +GAGATCATTGCTCTATGTGAATTTGAAAATATTATGACATCAAAAAGAGTAATAATACCAACCTATCTAA +GATCAATCAGTGTCAAAAACAAAGATCTGAACTCACTGGAAAATATAGCAACCACCGAATTCAAAAATGC +TATCACCAATGCTAAAATTATTCCCTATGCAGGATTAGTGTTAGTTATCACGGTTACTGATAATAAAGGA +GCATTCAAGTATATCAAGCCACAGAGTCAATTTATAGTGGATCTTGGTGCCTACCTAGAAAAAGAGAGCA +TATATTATGTGACTACTAATTGGAAGCATACAGCTACACGTTTTTCAATCAAACCACTAGAGGATTAAAC +TCAATTATCAACATTGAATGACAGGTTCACATATATCCTCAACTGCACACTATATCTAAACATCATAAAC +ATCTACACTACACACTTCATCACACAAACCAATCCCACTCAAAATCTAAAATCACTTCCAGCCATTGTCT +GCCAGACCTAGAGTGCGAATAGGTAAATAAAACAAGAATATGGGGTAAATAGATATCAGTTAGAGTTCAA +CCAATCTCAACAACCATCTATACCGCCAATCCAATACATACATTGCAAATCTTAAAATGGGAAACACATC +CATCACAATAGAATTCACAAGCAAATTTTGGCCCTATTTTACACTAATACATATGATCTTAACTCTAATC +TCTTTACTAATTATAATCACTATTATGATTGCAATACTAAATAAGCTAAGTGAACATAAAATATTCTGCA +ACAAAACTCTTGAACAAGGACAGATGTATCAAATCGACACATAGTGTTCTCCCATTATGCTGTATCAAAT +CACAATCCTGTGTATATAAATAAACAAATCCAATCTTCTCACAGAGTCATGGCATCACAAAACCATGCCA +ACCATCATGGTAGCATAGAGTAGTTATTAAAAATTAACATAATGATGAATTATTAGTATGGGATCAAAAA +CAACATTGGGGCAAATGCAACAATGTCCAAAAACAAGAATCAACGCACTGCCAGGACTCTAGAAAAGACC +TGGGATACTCTTAATCATCTAATTGTAATATCCTCTTGTTTATACAAATTAAATTTAAAATCTATAGCAC +AAATAGCACTATCAGTTTTGGCAATGATAATCTCAACCTCTCTTATAATTGCAGCCATAATATTCATCAT +CTCTGCCAATCACAAAGTTACACTAACAACTGTCACAGTTCAAACAATAAAAAACCACACTGAGAAAAAC +ATAACCACTTACCTCACTCAAGTCTCACCAGAAAGGGTTAGCCCATCCAAACAACCCACAGCCACACCAC +CAATCCACACAAACTCAGCCACAATATCACCCAATACAAAATCAGAAACACACCATACAACAACACAAAC +CAAAGGCACAATCTCTACTCCAACACAGAACAACAAGCCAAGCACAAAACCACGTCCAAAAAATCCACCA +AAAAAAGATGATTACCATTTTGAAGTGTTCAACTTTGTTCCCTGTAGTATATGTGGCAACAATCAACTCT +GCAAATCCATTTGCAAAACAATACCAAGCAATAAACCAAAGAAAAAACCAACTACAAAACCCACAAACAA +ACCACCTACCAAAACCACAAACAAAAGAGACCCCAAAACACTAGCCAAAACACCGAAAAAAGAAACCACC +ATTAACCCAACAAAAAAACCAACCCCCAAGACTACAGAAAGAGACACCAGCACCCCACAATCCACTGTGC +TCGACATAACCACATCAAAACACACAGAAAGGGACACCAGCACCTCACAATCCATTGCGCTTGACACAAC +CACATCAAAACACACAACCCAACAGCAATCTCTCTACTCAACCATCCCCGAAAACACACCCAACTCCACA +CAAACACCCACAGCATCCGAGCCCTCCACATCAAATTCTATCTAAAGACTCCAGTCATATGCTTAGTTAT +TTAAAAACTACATCTTAGCAAAGAACCGTGATCCCTCAAGCAAGAACGAAATTAAATCTGGGGCAAATAA +CCATGGAGTTGCTGATCCATAGATCAAGTGCAATCTTCCTAACTCTTGCTATTAATGCATTGTACCTTAC +CTCAAGTCAGAACATAACTGAGGAGTTTTACCAATCAACATGTAGTGCAGTTAGCAGAGGTTACTTGAGT +GCTTTAAGAACAGGTTGGTATACCAGTGTCATAACAATAGAATTAAGTAATATAAAAGAAACCAAATGCA +ATGGAACTGACACTAAAGTTAAACTTATAAAACAAGAATTAGATAAGTATAAGAATGCAGTAACTGAATT +ACAGTTACTTATGCAAAACACACCAGCTGTCAACAACCGGGCCAGAAGAGAAGCACCACAGTATATGAAC +TACACAATCAATACCACTAAAAACCTAAATGTATCAATAAGCAAGAAGAGGAAACGAAGATTTCTGGGCT +TCTTGTTAGGTGTAGGATCTGCAATAGCAAGTGGTATAGCTGTATCCAAAGTTCTACACCTTGAAGGAGA +AGTGAACAAGATCAAAAATGCTTTGCAGCTTACAAACAAAGCTGTAGTCAGTCTATCAAATGGGGTCAGT +GTTTTAACCAGCAGAGTGTTAGATCTCAAGAATTATATAAACAACCAATTATTACCTATGGTAAATCGAC +AGAGTTGTCGCATATCCAACATTGAGACAGTTATAGAATTCCAGCAGAAGAACAGCAGATTGTTGGAAAT +CACCAGAGAATTTAGTGTCAATGCAGGTGTAACGACACCTTTAAGCACTTACATGTTAACAAACAGTGAG +TTACTATCATTAATCAATGATATGCCTATAACAAATGATCAGAAAAAATTAATGTCAAGCAATGTTCAGA +TAGTAAGGCAACAAAGTTATTCTATCATGTCTATAATAAAGGAAGAAGTTCTTGCATATGTTGTACAGCT +ACCTATCTATGGTGTAATTGATACACCTTGCTGGAAATTACACACATCACCTCTGTGCACCACCAACATC +AAAGAAGGATCAAATATTTGTTTAACAAGGACTGATAGAGGATGGTATTGTGATAATGCAGGATCAGTAT +CCTTCTTTCCACAAGCTGACACTTGTAAAGTACAGTCCAATCGAGTATTTTGTGACACTATGAACAGTTT +GACATTACCAAGTGAAGTCAGCCTTTGTAACACTGACATATTCAATTCCAAGTATGACTGCAAAATTATG +ACATCAAAAACAGACATAAGCAGCTCAGTAATTACTTCTCTAGGAGCTATAGTGTCATGCTATGGTAAGA +CTAAATGTACTGCATCCAACAAAAATCGTGGAATTATAAAGACATTTTCTAATGGTTGTGATTATGTGTC +AAACAAAGGAGTAGATACTGTATCAGTGGGCAACACTCTATATTATGTCAACAAGCTGGAAGGCAAAAAC +CTTTATGTAAAAGGGGAACCTATAATAAATTACTATGACCCTCTAGTGTTTCCTTCTGATGAGTTTGATG +CATCAATATCTCAAGTCAATGAAAAAATTAATCAAAGTTTAGCTTTTATTCGTAGATCTGATGAATTATT +ACATAATGTAAATACTGGAAAATCTACTACAAATATTATGATAACTGCAATTATTATAGTAATCATTGTA +GTATTGTTATCATTAATAGCTATTGGTTTACTGTTGTATTGCAAAGCCAAAAACACACCAGTTACATTAA +GCAAAGACCAACTAAGTGGAATCAATAATATTGCATTCAGCAAATAGACAAAAAACCACCTGATCATGTT +CCAACAACAATCTGCTGACCATCAATCCCAAATCAACTTACAACAGATACTTCAACATCACAGCACAGGC +TGAATCATCTCCTCGCATCATGCTACCCACACAACTAAGCTAGATCCTTAATTCATAGTTACATAAAAGC +CTCAAATATCGCAATCAACACTAAATCAACACATCATTCACAAAACTAACAGCTGGGGCAAATATGTCGC +GAAGAAATCCCTGCAAATTTGAGATTAGAGGTCATTGCTTGAATGGTAGAAGATGCCACTACAGTCATAA +TTACTTTGAATGGCCTCCTCATGCATTGCTAGTGAGGCAAAACTTCATGTTAAACAAGATACTCAAGTCA +ATGGACAAGAGCATAGACACTTTGTCTGAAATAAGTGGAGCTGCTGAACTTGATAGAACAGAAGAATATG +CTCTTGGTATAGTTGGAGTGCTAGAGAGTTACATAGGATCTATAAACAACATAACAAAACAATCAGCATG +TGTTGCTATGAGTAAACTTCTTATTGAGATCAATAGTGATGACATTAAAAAGCTGAGAGATAATGAAGAA +CCCAATTCACCTAAGATAAGAGTGTACAATACTGTTATATCATACATCGAGAGCAATAGAAAAAACAGCA +AGCAAACCATCCATCTGCTTAAACGATTACCAGCAGACGTGCTGAAGAAGACAATAAAGAACACATTAGA +TATCCACAAAAGCATAACCATAAGCAACCCAAAAGAGTCAACCATAAGTGATCAAAATGACCAAACCAAA +AATAATGATATTACCGGATAAATATCCTTGTAGTATATCATCCATATTGATCTCAAGTGAAAGCATGATT +GCTACATTCAATCATAAAGACATATTACAATTTAACCACAACCATTTAGATAACCACCAGTGTTTATTAA +ATCATATATTTGATGAAATTCATTGGACACCTAAAAACTTATTAGATGCCACTCAACAATTTCTCCAACA +TCTTAACATCCCTGAAGATATATATACAGTATATATATTAGTGTCATAATGCTTGATCATAGCGACTCTA +TATCATCCAACCATAAATTAGTCTTAATAAAGTTATGGGACAAAATGGATCCCATTATTAATGGAAGCTC +CGCTAATGTATATCTAACTGATAGTTATCTAAAAGGTGTTATCTCTTTTTCAGAATGTAATGCTTTAGGG +AGTTACCTTTTTAACGGCCCTTATCTTAAAAATGATTATACCAACTTAATTAGTAGACAAAGCCCACTAA +TAGAGCATATGAATCTAAAAAAACTAACTATAACACAGTCATTAATATCTAGATACCATAAAGGCGAACT +GAAATTAGAAGAACCAACTTATTTCCAGTCATTACTTATGACATATAAAAGCATGTCCTCGTCTGAACAA +ATTGCTACAACTAACTTACTTAAAAAAATAATACGAAGAGCTATAGAAATAAGTGATGTAAAGGTGTACG +CCATCTTGAATAAACTAGGACTAAAGGAAAAGGACAGAGTTAAGCCCAACAACAATTCAGGTGATGAAAA +CTCAGTACTTACAACCATAATTAAAGATGATATACTCTCAGCTGTGGAAAACAATCAATCATATACAAAT +TCAGATAAAAATTACTCAGTAAATCAAAATATCAATATCAAAACAACACTCTTAAAAAAGTTGATGTGTT +CAATGCAACATCCTCCATCATGGTTAATACACTGGTTCAATTTATATACAAAATTAAATAACATATTAAC +ACAATATCGATCAAATGAGGTAAAAAGTCATGGGTTTATATTAATAGATAATCAAACTTTGAGTGGTTTT +CAGTTTATTTTAAATCAATATGGTTGCATTGTTTATCATAAAGGGCTCAAAAAAATTACAACTACTACAT +ACAATCAATTTTTGACATGGAAAGACATCAGCCTCAGCAGATTAAATGTTTGCTTAATTACTTGGATAAG +TAATTGTTTAAATACATTAAATAAAAGCTTAGGGTTGAGATGCGGATTCAATAATGTTGTGCTATCACAA +TTATTCCTTTACGGAGATTGTATACTGAAATTATTTCATAATGAAGGATTTTACATAATAAAAGAAGTAG +AAGGATTTATTATGTCTTTAATTCTAAACATAACAGAAGAAGATCAATTTAGGAAACGATTTTATAATAG +CATGCTAAATAACATCACAGATGCAGCTATTAAGGCTCAAAAGGATCTACTATCAAGAGTATGTCACACT +TTATTAGACAAGACAGTGTCTGATAATATCATAAATGGTAAATGGATAATTCTATTAAGTAAATTTCTTA +AATTGATTAAGCTTGCAGGTGATAATAATCTCAATAACTTGAGTGAGCTATATTTTCTCTTCAGAATCTT +TGGACATCCAATGGTTGATGAAAGACAAGCAATGGATGCTGTAAGAATTAACTGCAATGAAACTAAGTTC +TATTTATTAAGTAGCCTAAGTACGTTGAGAGGTGCTTTCATTTATAGAATCATAAAAGGGTTTGTAAATA +CCTACAATAGATGGCCCACTTTAAGGAATGCTATTGTCCTACCTCTAAGATGGTTAAACTATTATAAACT +TAATACTTATCCATCTCTACTTGAAATCACAGAAAATGATTTGATTATTTTATCAGGATTGCGGTTCTAT +CGTGAGTTTCATCTGCCTAAAAAAGTGGATCTTGAAATGATAATAAATGACAAAGCTATTTCTCCTCCAA +AAGATCTAATATGGACTAGTTTTCCTAGAAATTACATGCCATCACATATACAAAATTATATAGAACATGA +AAAGTTGAAGTTCTCTGAAAGCGACAGATCAAGAAGAGTACTAGAGTATTACTTGAGAGATAATAAATTC +AATGAATGTGATCTATACAATTGTGTAGTTAATCAAAGCTATCTCAACAACTCTAATCATGTGGTATCAC +TAACTGGTAAAGAAAGAGAGCTCAGTGTGGGTAGAATGTTTGCTATGCAACCAGGTATGTTTAGGCAAAT +CCAAATCTTAGCAGAAAAAATGATAGCTGAAAATATTTTACAATTCTTCCCTGAGAGTTTGACAAGATAT +GGTGATCTAGAGCTTCAAAAGATATTAGAATTAAAAGCAGGAATAAGCAACAAGTCAAATCGTTATAATG +ATAACTACAACAATTATATCAGTAAATGTTCTATAATAACAGATCTTAGCAAATTTAATCAAGCATTTAG +ATATGAAACATCATGTGTCTGCAGTGATGTATTAGATGAACTGCATGGGGTACAATCTCTATTCTCTTGG +TTGCATTTAACAATACCTCTTGTCACAATAATATGTACATATAGACATGCACCTCCTTTTATAAAGGATC +ATGTTGTCAATCTTAATGAAGTTGATGAACAAAGTGGGTTATACAGATATCATATGGGTGGTATTGAGGG +CTGGTGTCAAAAACTGTGGACCATTGAAGCCATATCATTATTAGATCTAATATCTCTTAAAGGTAAATTC +TCCATCACAGCTCTGATAAATGGTGATAATCAGTCAATTGATATAAGTAAACCAGTTAGACTTATAGAGG +GTCAGACCCATGCTCAAGCAGATTATTTGTTAGCATTAAATAGCCTTAAGTTGCTATATAAAGAGTATGC +AGGCATAGGCCATAAGCTTAAGGGAACCGAGACCTATATATCTCGAGATATGCAGTTCATGAGCAAAACA +ATCCAGCACAATGGAGTGTACTATCCAGCCAGTATCAAAAAAGTCCTGAGAGTAGGTCCATGGATAAATA +CAATACTTGATGATTTTAAAGTTAGTTTAGAATCTATAGGTAGCTTAACACAGGAGTTAGAATACAGAGG +AGAAAGCTTATTATGCAGTTTAATATTTAGGAATATTTGGTTATACAATCAAATTGCTCTGCAACTCCGG +AATCATGCTTTATGTAATAATAAGCTATATTTAGATATATTGAAAGTATTAAAACACTTAAAAACCTTTT +TTAATCTTGATAGTATCGATACGGCATTATCATTGTATATGAACTTGCCTATGCTGTTTGGTGGTGGTGA +TCCTAATTTGTTATATCGAAGCTTTTATAGGAGAACTCCAGACTTCCTTACAGAAGCTATAGTACATTCA +GTGTTTGTGTTGAGCTATTATACTGGTCACGATCTACAAGATAAGCTCCAGGATCTTCCAGATGATAGAC +TGAACAAATTCTTGACTTGTGTCATCACATTTGATAAAAATCCAAATGCCGAGTTTGTAACATTGATGAG +GGATCCACAGGCTTTAGGGTCTGAAAGGCAAGCTAAAATTACTAGTGAGATTAATAGATTAGCAGTAACA +GAAGTCTTAAGTATAGCTCCAAACAAAATATTTTCTAAAAGTGCGCAACACTATACTACCACTGAGATTG +ATCTAAATGACATTATGCAAAATATAGAACCAACTTACCCTCATGGATTAAGAGTTGTTTATGAAAGTTT +ACCTTTTTATAAAGCAGAAAAAATAGTTAATCTTATATCAGGAACAAAATCCATAACTAATATACTTGAA +AAAACATCAGCGATAGATACAACTGATATTAATAGGGCTACTGATATGATGAGGAAAAATATAACCTTAC +TTATAAGGATACTTCCACTAGATTGTAACAAAGACAAAAGAGAGTTATTAAGTTTAGAAAATCTTAGCAT +AACTGAATTAAGCAAGTATGTAAGAGAAAGATCTTGGTCATTATCCAATATAGTAGGAGTAACATCACCA +AGTATTATGTTCACAATGGACATTAAATATACAACTAGCACTATAGCCAGTGGTATAATTATAGAAAAAT +ATAATGTTAATGGTTTAACTCGTGGTGAAAGAGGACCTACTAAGCCATGGGTAGGTTCATCTACACAAGA +GAAAAAAACAATGCCAGTGTACAATAGACAAGTTTTAACCAAAAAGCAAAGAGACCAAATAGATTTATTA +GCAAAATTAGACTGGGTATATGCATCCATAGACAACAAAGATGAATTCATGGAAGAACTGAGTACTGGAA +CACTTGGACTGTCATATGAAAAGGCCAAAAAGTTGTTTCCACAATATCTAAGTGTCAATTATTTACACCG +GTTAACAGTCAGTAGTAGACCATGCGAATTCCCTGCCTCAATACCAGCTTATAGAACAACAAATTATCAT +TTTGATACTAGTCCTATCAATCATGTATTAACAGAAAAGTATGGAGATGAAGATATCGACATTGTGTTTC +AAAATTGCATAAGTTTTGGTCTTAGCTTGATGTCAGTTGTGGAACAATTCACAAACATATGTCCTAATAG +AATTATTCTCATACCGAAGCTGAATGAGATACATTTGATGAAACCTCCTATATTTACAGGAGATGTTGAT +ATCATCAAGTTGAAGCAAGTGATACAAAAACAGCATATGTTCCTACCAGATAAAATAAGTTTAACCCAAT +ATGTAGAATTATTCTTAAGTAACAAAGCACTTAAATCTGGATCTCACATCAACTCTAATTTAATATTAGC +ACATAAAATGTCTGATTATTTTCATAATGCGTATATTTTAAGTACTAATTTAGCTGGACATTGGATTCTG +ATTATTCAACTTATGAAAGATTCAAAAGGTATTTTTGAAAAAGATTGGGGAGAGGGGTATATAACTGATC +ATATGTTCATTAATTTGAATGTTTTCTTTAATGCTTATAAGACTTATTTGCTATGTTTTCATAGAGGTTA +TGGTAAAGCAAAATTAGAATGTGATATGAACACTTCAGATCTTCTTTGTGTTTTGGAGTTAATAGACTGT +AGCTACTGGAAATCTATGTCTAAAGTTTTCCTAGAACAAAAAGTCATAAAATACATAGTCAATCAAGACA +CAAGTTTGCATAGAATAAAAGGTTGTCACAGTTTTAAGTTGTGGTTTTTAAAACGCCTTAATAATGCTAA +ATTTACCGTATGCCCTTGGGTTGTTAACATAGATTATCACCCAACACACATGAAAGCTATATTATCTTAC +ATAGATTTAGTTAGAATGGGGTTAATAAATGTAGATAAATTAACCATTAAAAATAAAAACAAATTCAATG +ATGAATTTTACACATCAAATCTCTTTTACATTAGTTACAACTTTTCAGACAACACTCATCTGCTAACAAA +ACAAATAAGGATTGCTAATTCAGAATTAGAAGATAATTATAACAAACTATATCACCCAACCCCAGAAGCT +TTAGAAAATGTATCATTAATCCCTGTTAAAAGTAATAATAGAAACAAACCTAAATTTTGTATAAGTGGAA +GTACTGAATCTATGATGACGTCAACATTCTCTAATAAAATGCATATTAAATCTTCCACTGTTACCACAAG +ATTCAATTATAGCAGACAAGACTTGTACAATTTATTTCCAATTGTTGTGATAGACAGGATTATAGATCAT +TCAGGTAATACAGAAAAATCTAACCAACTTTACACCACCACTTCACATCAGACATCTTTAGTAAGGAACA +GTGCATCACTTTATTGCATGCTTCCTTGGCATCATGTCAATAGATTTAACTTTGTATTTAGTTCCACAGG +ATGCAAGATCAGTATAGAATATATTTTAAAAGATCTTAAGATTAAAGATCCCAGTTGCATAGCATTCATA +GGTGAAGGAGCTGGTAACTTATTATTACGTACGGTAGTAGAACTTCATCCTGACATAAGATATATTTACA +GAAGTTTAAAAGATTGCAATGATCATAGTTTACCTATTGAATTTCTAAGGTTATACAACGGGCATATAAA +CATAGATTATGGTGAGAATTTAACCATTCCTGCTACAGATGCAACTAACAACATACATTGGTCTTATTTA +CACATAAAATTTGCAGAACCTATTAGTATCTTTGTCTGTGATGCTGAATTACCTGTCACAGCCAATTGGA +GTAAGATCATAATTGAATGGAGTAAGCATGTAAGAAAGTGCAAATACTGTTCTTCTGTAAATAGATGCAT +TTTAATTGCAAAATACCATGCTCAAGATGATATTGATTTCAAATTAGATAACATTACTATATTAAAAACT +TATGTGTGCCTAGGTAGCAAGTTAAAAGGATCTGAAGTTTACTTAGTCCTTACAATAGGCCCTGCAAATA +TACTTCCTGTTTTTGATGTTGTGCAAAATGCTAAATTGATTCTTTCAAGAACTAAAAATTTCATTATGCC +TAAAAAGATTGACAAGGAATCTATCGATGCAAATATTAAAAGCTTAATACCTTTCCTTTGTTACCCTATA +ACAAAAAATGGAATTAAGACTTCATTGTCAAAATTGAAGAGTGTAGTTAATGGAGATATATTATCATATT +CTATAGCTGGACGTAATGAAGTATTCAGCAACAAGCTTATAAACCACAAGCATATGAATATCTTAAAATG +GCTGGATCATGTTTTAAACTTTAGATCAGCTGAACTTAATTACAATCATTTATACATGATAGAGTCCACA +TATCCTTACTTGAGTGAATTATTAAATAGTTTAACAACCAATGAGCTCAAGAAGCTGATTAAAATAACAG +GTAGTGTACTATACAACCTTCCTAATGAACAGTAACTTAAAATATCATTAACAAGTTTGGTCAAATTTAG +ATGCTAACACATTATTATATTATAGTTATTAAAAAATATGCAAACTTTTCAATAATTTAGCATATTGATT +CCAAAATTATCATTTTAGTCTTAAGGGATTAAATAAAAGTCTAAAACTAACAATCACACATGTGCATTTA +CAACACAACGAGACATTAGTTTTTGACACTTTTTTTCTCGTGGCCGGCATG + diff --git a/resources/rsvb/RSVB_inserts_400_V2.1.bed b/resources/rsvb/RSVB_inserts_400_V2.1.bed new file mode 100644 index 00000000..26a46911 --- /dev/null +++ b/resources/rsvb/RSVB_inserts_400_V2.1.bed @@ -0,0 +1,51 @@ +MT107528.1 141 519 scheme_INSERT_1 pool1 + +MT107528.1 434 813 scheme_INSERT_2 pool2 + +MT107528.1 763 1147 scheme_INSERT_3 pool1 + +MT107528.1 1022 1385 scheme_INSERT_4 pool2 + +MT107528.1 1335 1713 scheme_INSERT_5 pool1 + +MT107528.1 1666 2046 scheme_INSERT_6 pool2 + +MT107528.1 1995 2370 scheme_INSERT_7 pool1 + +MT107528.1 2257 2628 scheme_INSERT_8 pool2 + +MT107528.1 2580 2941 scheme_INSERT_9 pool1 + +MT107528.1 2758 3136 scheme_INSERT_10 pool2 + +MT107528.1 3085 3467 scheme_INSERT_11 pool1 + +MT107528.1 3420 3803 scheme_INSERT_12 pool2 + +MT107528.1 3695 4067 scheme_INSERT_13 pool1 + +MT107528.1 3981 4358 scheme_INSERT_14 pool2 + +MT107528.1 4144 4515 scheme_INSERT_15 pool1 + +MT107528.1 4483 4862 scheme_INSERT_16 pool2 + +MT107528.1 4847 5214 scheme_INSERT_17 pool1 + +MT107528.1 5136 5459 scheme_INSERT_18 pool2 + 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