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MHH-RCUG / Wochenende

Deprecated see https://github.com/MHH-RCUG/nf_wochenende : A whole Genome/Metagenome Sequencing Alignment Pipeline in Python3
https://github.com/MHH-RCUG/nf_wochenende
MIT License
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extract viral reads from bam #118

Closed colindaven closed 3 years ago

colindaven commented 3 years ago
colindaven commented 3 years ago

Current viruses in reference 2021_02 which can be extracted for fine scaled plotting withextract_viral_reads.sh

less viruses_2021_02.bed 
NC_006273.2_Human_herpesvirus_5_strain_Merlin__complete_genome  1       235646
NC_001664.4_Human_betaherpesvirus_6A__variant_A_DNA__complete_virion_genome__isolate_U1102      1       159378
NC_000898.1_Human_herpesvirus_6B__complete_genome       1       162114
NC_001716.2_Human_herpesvirus_7__complete_genome        1       153080
NC_003461.1_Human_parainfluenza_virus_1__complete_genome        1       15600
NC_001796.2_Human_parainfluenza_virus_3__complete_genome        1       15462
NC_002645.1_Human_coronavirus_229E__complete_genome     1       27317
NC_005831.2_Human_Coronavirus_NL63__complete_genome     1       27553
NC_001498.1_Measles_virus__complete_genome      1       15894
NC_001803.1_Respiratory_syncytial_virus__complete_genome        1       15191
NC_002200.1_Mumps_virus__complete_genome        1       15384
NC_001348.1_Human_herpesvirus_3__complete_genome        1       124884
NC_001798.2_Human_herpesvirus_2_strain_HG52__complete_genome    1       154675
NC_006577.2_Human_coronavirus_HKU1__complete_genome     1       29926
NC_001806.2_Human_herpesvirus_1_strain_17__complete_genome      1       152222
NC_001897.1_Human_parechovirus__genome  1       7348
NC_001612.1_Human_enterovirus_A__complete_genome        1       7413
NC_004718.3_SARS_coronavirus_Tor2__complete_genome      1       29751
NC_012042.1_Human_bocavirus_2c_PK_isolate_PK_5510__complete_genome      1       5196
NC_019843.3_Middle_East_respiratory_syndrome_related_coronavirus_isolate_HCoV_EMC_2012__complete_genome 1       30119
NC_021928.1_Human_parainfluenza_virus_4a_viral_cRNA__complete_genome__strain_M_25       1       17052
NC_007605.1_Human_gammaherpesvirus_4__complete_genome   1       171823
NC_039199.1_Human_metapneumovirus_isolate_00_1__complete_genome 1       13350
NC_038311.1_Human_rhinovirus_1_strain_ATCC_VR_1559__complete_genome     1       7137
NC_006213.1_Human_coronavirus_OC43_strain_ATCC_VR_759__complete_genome  1       30741
NC_045512.2_Severe_acute_respiratory_syndrome_coronavirus_2_isolate_Wuhan_Hu_1__complete_genome 1       29903
NC_002204.1_Influenza_B_virus_RNA_1__complete_sequence  1       14452
NC_005222.1_Hantaan_virus_segment_L__complete_genome    1       11845
NC_006307.2_Influenza_C_virus__C_Ann_Arbor_1_50_        1       12906
NC_007373.1_Influenza_A_virus__A_New_York_392_2004_H3N2__       1       13627
NC_002023.1_Influenza_A_virus__A_Puerto_Rico_8_1934_H1N1__      1       13588
colindaven commented 3 years ago

Completed with https://github.com/MHH-RCUG/Wochenende/pull/119