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  1. Mar 14, 2025
  2. Mar 12, 2025
    • Fanny Wegner's avatar
      Update 137 files · a84d58dd
      Fanny Wegner authored
      - /exercises/Assemblies/.gitkeep
      - /exercises/Assemblies/EcAssemblies.zip
      - /exercises/Assemblies/EcP1U1122-illumina.fna
      - /exercises/Assemblies/EcP1U1122_ONTmedaka.fna
      - /exercises/Assemblies/EcP1U1122_hybrid.fna
      - /exercises/Assemblies/EcP2B1122-illumina.fna
      - /exercises/Assemblies/EcP2B1122_ONTmedaka.fna
      - /exercises/Assemblies/EcP2B1122_hybrid.fna
      - /exercises/Assemblies/EcP2U1122-illumina.fna
      - /exercises/Assemblies/EcP2U1122_ONTmedaka.fna
      - /exercises/Assemblies/EcP2U1122_hybrid.fna
      - /exercises/Assemblies/EcP31122_ONTmedaka.fna
      - /exercises/Assemblies/EcP3U1122-illumina.fna
      - /exercises/Assemblies/EcP3U1122_hybrid.fna
      - /exercises/Assemblies/SaAssemblies.zip
      - /exercises/Assemblies/SaH1P10622-illumina.fna
      - /exercises/Assemblies/SaH1P10622_ONTmedaka.fna
      - /exercises/Assemblies/SaH1P10622_hybrid.fna
      - /exercises/Assemblies/SaH1P30922-illumina.fna
      - /exercises/Assemblies/SaH1P30922_ONTmedaka.fna
      - /exercises/Assemblies/SaH1P30922_hybrid.fna
      - /exercises/Assemblies/SaH1P41122-illumina.fna
      - /exercises/Assemblies/SaH1P41122_ONTmedaka.fna
      - /exercises/Assemblies/SaH1P41122_hybrid.fna
      - /exercises/Assemblies/SaH1P51022-illumina.fna
      - /exercises/Assemblies/SaH1P51022_hybrid.fna
      - /exercises/Assemblies/SaH2P60722-illumina.fna
      - /exercises/Assemblies/SaH2P60722_ONTmedaka.fna
      - /exercises/Assemblies/SaH2P60722_hybrid.fna
      - /exercises/Assemblies/SaH2P70722-illumina.fna
      - /exercises/Assemblies/SaH2P70722_ONTmedaka.fna
      - /exercises/Assemblies/SaH2P70722_hybrid.fna
      - /exercises/Assemblies/SaH2P80822-illumina.fna
      - /exercises/Assemblies/SaH2P80822_ONTmedaka.fna
      - /exercises/Assemblies/SaH2P80822_hybrid.fna
      - /exercises/Assemblies/SaH2P90822-illumina.fna
      - /exercises/Assemblies/SaH2P90822_ONTmedaka.fna
      - /exercises/Assemblies/SaH2P90822_hybrid.fna
      - /exercises/fastqs/.gitkeep
      - /exercises/fastqs/2022187369_staaur.fastq
      - /exercises/fastqs/EcP1U1122_R1.fastq.gz
      - /exercises/fastqs/EcP1U1122_R2.fastq.gz
      - /exercises/fastqs/EcP2B1122_R1.fastq.gz
      - /exercises/fastqs/EcP2B1122_R2.fastq.gz
      - /exercises/fastqs/EcP2U1122_R1.fastq.gz
      - /exercises/fastqs/EcP2U1122_R2.fastq.gz
      - /exercises/fastqs/EcP3U1122_R1.fastq.gz
      - /exercises/fastqs/EcP3U1122_R2.fastq.gz
      - /exercises/fastqs/SaH1P10622_R1.fastq.gz
      - /exercises/fastqs/SaH1P10622_R2.fastq.gz
      - /exercises/fastqs/SaH2P80822_R1.fastq.gz
      - /exercises/fastqs/SaH2P80822_R2.fastq.gz
      - /exercises/Pangenome_analysis/.gitkeep
      - /exercises/Pangenome_analysis/Pangenome.md
      - /exercises/Pangenome_analysis/Pangenome.pdf
      - /exercises/Pangenome_analysis/panaroo.sh
      - /exercises/Primer_design/.gitkeep
      - /exercises/Primer_design/PapG_aln_BK.fasta
      - /exercises/QC_nanopore/.gitkeep
      - /exercises/QC_nanopore/230320SP_SP_TR_Excercise_fastq_QC.pdf
      - /exercises/QC_nanopore/qc_mrsa.zip
      - /exercises/QC_nanopore/qc_upec.zip
      - /exercises/Tablet_genome_browser/.gitkeep
      - /exercises/Tablet_genome_browser/SaH1P10622.gff
      - /exercises/Tablet_genome_browser/SaH1P10622.vcf
      - /exercises/Tablet_genome_browser/SaH1P10622_alignment.removed_duplicates.bam
      - /exercises/Tablet_genome_browser/SaH1P10622_alignment.removed_duplicates.bam.bai
      - /exercises/Tablet_genome_browser/SaH1P10622_assembly.fasta
      - /exercises/Typing_cgMLST/.gitkeep
      - /exercises/Typing_cgMLST/EcAssemblies.zip
      - /exercises/Typing_cgMLST/EcP1U1122.fna
      - /exercises/Typing_cgMLST/EcP2B1122.fna
      - /exercises/Typing_cgMLST/EcP2U1122.fna
      - /exercises/Typing_cgMLST/EcP3U1122.fna
      - /exercises/Typing_cgMLST/SaAssemblies.zip
      - /exercises/Typing_cgMLST/SaH1P10622.fna
      - /exercises/Typing_cgMLST/SaH1P30922.fna
      - /exercises/Typing_cgMLST/SaH1P41122.fna
      - /exercises/Typing_cgMLST/SaH1P51022.fna
      - /exercises/Typing_cgMLST/SaH2P60722.fna
      - /exercises/Typing_cgMLST/SaH2P70722.fna
      - /exercises/Typing_cgMLST/SaH2P80822.fna
      - /exercises/Typing_cgMLST/SaH2P90822.fna
      - /exercises/Typing_cgMLST/pathogenwatch-metadata-template-esccol.csv
      - /exercises/Typing_cgMLST/pathogenwatch-metadata-template-staaur.csv
      - /exercises/Typing_cgMLST_SpareFiles/.gitkeep
      - /exercises/Typing_cgMLST_SpareFiles/Esccol_GrapeTree_BIGSdb_916412_9814689309_05652.tar
      - /exercises/Typing_cgMLST_SpareFiles/Esccol_iTOL_BIGSdb_926019_8573951579_61086.tar
      - /exercises/Typing_cgMLST_SpareFiles/MRSAGrapetree_BIGSdb_3009469_0829304420_90518.tar
      - /exercises/Typing_cgMLST_SpareFiles/MRSAiTOL_BIGSdb_3009469_3861660682_86066.tar
      - /exercises/Typing_cgMLST_SpareFiles/Pasteur_upload_template_Ecoli.xlsx
      - /exercises/Typing_cgMLST_SpareFiles/PubMLST_upload_template_Saureus.xlsx
      - /exercises/Visualisation_Phandango/.gitkeep
      - /exercises/Visualisation_Phandango/Ecoli_metadata_Phandango.csv
      - /exercises/Visualisation_Phandango/IQtree_hybrid_noref.treefile.tre
      - /exercises/Visualisation_Phandango/Saureus_metadata_Phandango.csv
      - /exercises/230331_Blockkurs_HSS_MetadataExercise.pdf
      - /exercises/230410_Blockkurs_TR_PrimerDesign2.pdf
      - /exercises/240323_Blockkurs_HSS_cgMLSTExercise.pdf
      - /exercises/240323_Blockkurs_HSS_MLSTExercise.pdf
      - /exercises/240409_Blockkurs_ZG_ResVirExercise.pdf
      - /exercises/abricate_exercise.md
      - /exercises/assembly_exercise.md
      - /exercises/ompA.zip
      - /exercises/phylo_exercise.md
      - /exercises/qc_exercise.md
      - /exercises/UNIX_HPC_cheat_sheet.md
      - /exercises/UNIX_HPC_exercise_instructions.md
      - /assignments/240315_HSS_TR_Assignment_week1.pdf
      - /assignments/240322_Blockkurs_HSS_TypingMethodsAssignment.pdf
      - /assignments/240410_Blockkurs_AnalysisAssignment.pdf
      - /slides/24-03-28_JC_MRSA_ES.pptx
      - /slides/2013__Whole-genome_sequencing_of_MRSA_babies__Harris__flat.pdf
      - /slides/230412_Blockkurs_TR_SummaryFeedback.pdf
      - /slides/230412_Blockkurs_TR_SummaryFeedback.pptx
      - /slides/240314_Blockkurs_Egli_Intro_hss-on.pdf
      - /slides/240315_TR_Intro_to_QC.pdf
      - /slides/240319_intro_unix_containers.pdf
      - /slides/240320_SP_TR_Assembly.pdf
      - /slides/240321_Blockkurs_HSS_Typing.pdf
      - /slides/240321_TR_Assembly_QC.pdf
      - /slides/240322_Blockkurs_HSS_cgMLST.pdf
      - /slides/240323_Blockkurs_HSS_TypingDiscussion.pdf
      - /slides/240327_intro_phylogenetics.pdf
      - /slides/240409_Blockkurs_HSS_VisualisingPhylogeniesMetadata.pdf
      - /slides/240409_TR_Identifying_resistance_and_virulence_factors.pdf
      - /slides/240410_Blockkurs_Bioinformatik_Lecture_Bacterial_Virulence_final.pdf
      - /slides/240410_Blockkurs_VB_Pangenome.pdf
      - /slides/240412_Blockkurs_Farewell.pdf
      - /slides/20240321_Unicycler_BIO296_ZG.pdf
      - /slides/20240322_blockkurs_journalclub_em.pdf
      - /slides/20240410_JournalClub_Virulence_and_Diagnostics_YG.pdf
      - /slides/Introduction_240314_TR.pdf
      - /slides/Introduction_projects_240314_TR.pdf
      - /slides/Library_prep_presentation_and_flowdiagram_SP.pdf
      - /slides/Routine_diagnostics_NGS_240314_TR.pdf
      - /slides/Sequencing_technologies_240314_TR.pdf
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