viral-ngs: genomic analysis pipelines for viral sequencing

Contents

• 1. Description of the methods
  • 1.1. Taxonomic read filtration
  • 1.2. Viral genome analysis
  • 1.3. Taxonomic read identification
• 2. Using the WDL pipelines
• 3. Submitting viral sequences to NCBI
  • 3.1. Register your BioProject
  • 3.2. Register your BioSamples
  • 3.3. Set up an NCBI author template
  • 3.4. Prepare requisite input files for your submission batches
  • 3.5. Run the genbank submission pipeline
• 4. WDL Workflows
  • 4.1. align_and_count_report
  • 4.2. align_and_count_multiple_report
  • 4.3. align_and_plot
  • 4.4. assemble_denovo
  • 4.5. assemble_denovo_metagenomic
  • 4.6. assemble_refbased
  • 4.7. augur_export_only
  • 4.8. augur_from_assemblies
  • 4.9. augur_from_beast_mcc
  • 4.10. augur_from_mltree
  • 4.11. augur_from_msa
  • 4.12. augur_from_msa_with_subsampler
  • 4.13. qiime_import_bam
  • 4.14. bams_multiqc
  • 4.15. beast_gpu
  • 4.16. megablast
  • 4.17. calc_bam_read_depths
  • 4.18. classify_kaiju
  • 4.19. classify_kraken2
  • 4.20. classify_krakenuniq
  • 4.21. classify_multi
  • 4.22. amplicon16S_analysis
  • 4.23. classify_single
  • 4.24. coverage_table
  • 4.25. CreateEntericsQCViz
  • 4.26. CreateEntericsQCVizGeneral
  • 4.27. demux_deplete
  • 4.28. demux_metadata_only
  • 4.29. demux_only
  • 4.30. demux_plus
  • 4.31. deplete_only
  • 4.32. detect_cross_contamination
  • 4.33. detect_cross_contamination_precalled_vcfs
  • 4.34. diff_genome_sets
  • 4.35. downsample
  • 4.36. dump_gcloud_env_info
  • 4.37. fastq_to_ubam
  • 4.38. fetch_annotations
  • 4.39. fetch_sra_to_bam
  • 4.40. filter_classified_bam_to_taxa
  • 4.41. filter_sequences
  • 4.42. genbank_gather
  • 4.43. genbank_single
  • 4.44. isnvs_lofreq
  • 4.45. isnvs_merge_to_vcf
  • 4.46. isnvs_one_sample
  • 4.47. kraken2_build
  • 4.48. mafft
  • 4.49. mafft_and_snp
  • 4.50. mafft_and_snp_annotated
  • 4.51. mafft_and_trim
  • 4.52. chunk_megablast
  • 4.53. merge_bams
  • 4.54. merge_metagenomics
  • 4.55. merge_tar_chunks
  • 4.56. merge_vcfs
  • 4.57. merge_vcfs_and_annotate
  • 4.58. metagenomic_denovo
  • 4.59. multiqc_only
  • 4.60. nextclade_single
  • 4.61. populate_library_and_sample_tables_from_flowcell
  • 4.62. reconstruct_from_alignments
  • 4.63. sarscov2_batch_relineage
  • 4.64. sarscov2_biosample_load
  • 4.65. sarscov2_data_release
  • 4.66. sarscov2_genbank
  • 4.67. genbank_dump
  • 4.68. sarscov2_gisaid_ingest
  • 4.69. sarscov2_illumina_full
  • 4.70. sarscov2_lineages
  • 4.71. sarscov2_nextclade_multi
  • 4.72. sarscov2_nextstrain
  • 4.73. sarscov2_nextstrain_aligned_input
  • 4.74. sarscov2_sequencing_reports
  • 4.75. sarscov2_sra_to_genbank
  • 4.76. scaffold_and_refine
  • 4.77. scaffold_and_refine_multitaxa
  • 4.78. submit_biosample
  • 4.79. submit_genbank
  • 4.80. submit_sra
  • 4.81. subsampler_only
  • 4.82. subsample_by_metadata
  • 4.83. subsample_by_metadata_with_focal
  • 4.84. terra_table_to_tsv
  • 4.85. terra_tsv_to_table
  • 4.86. update_data_tables
  • 4.87. trimal
  • 4.88. unpack_archive_to_bucket