viral-ngs: genomic analysis pipelines for viral sequencing¶
Contents¶
- 1. Description of the methods
- 2. Using the WDL pipelines
- 3. Submitting viral sequences to NCBI
- 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_refbased
- 4.6. augur_export_only
- 4.7. augur_from_assemblies
- 4.8. augur_from_beast_mcc
- 4.9. augur_from_mltree
- 4.10. augur_from_msa
- 4.11. augur_from_msa_with_subsampler
- 4.12. qiime_import_bam
- 4.13. bams_multiqc
- 4.14. beast_gpu
- 4.15. calc_bam_read_depths
- 4.16. classify_kaiju
- 4.17. classify_kraken2
- 4.18. classify_krakenuniq
- 4.19. classify_multi
- 4.20. amplicon16S_analysis
- 4.21. classify_single
- 4.22. contigs
- 4.23. coverage_table
- 4.24. demux_deplete
- 4.25. demux_metag
- 4.26. demux_only
- 4.27. demux_plus
- 4.28. deplete_only
- 4.29. detect_cross_contamination
- 4.30. detect_cross_contamination_precalled_vcfs
- 4.31. diff_genome_sets
- 4.32. downsample
- 4.33. fastq_to_ubam
- 4.34. fetch_annotations
- 4.35. fetch_sra_to_bam
- 4.36. filter_classified_bam_to_taxa
- 4.37. filter_sequences
- 4.38. genbank
- 4.39. isnvs_lofreq
- 4.40. isnvs_merge_to_vcf
- 4.41. isnvs_one_sample
- 4.42. kraken2_build
- 4.43. mafft
- 4.44. mafft_and_snp
- 4.45. mafft_and_snp_annotated
- 4.46. mafft_and_trim
- 4.47. merge_bams
- 4.48. merge_metagenomics
- 4.49. merge_tar_chunks
- 4.50. merge_vcfs
- 4.51. merge_vcfs_and_annotate
- 4.52. metagenomic_denovo
- 4.53. multiqc_only
- 4.54. nextclade_single
- 4.55. sarscov2_batch_relineage
- 4.56. sarscov2_biosample_load
- 4.57. sarscov2_data_release
- 4.58. sarscov2_genbank
- 4.59. genbank_dump
- 4.60. sarscov2_gisaid_ingest
- 4.61. sarscov2_illumina_full
- 4.62. sarscov2_lineages
- 4.63. sarscov2_nextclade_multi
- 4.64. sarscov2_nextstrain
- 4.65. sarscov2_nextstrain_aligned_input
- 4.66. sarscov2_sequencing_reports
- 4.67. sarscov2_sra_to_genbank
- 4.68. scaffold_and_refine
- 4.69. subsampler_only
- 4.70. subsample_by_metadata
- 4.71. subsample_by_metadata_with_focal
- 4.72. terra_table_to_tsv
- 4.73. update_data_tables
- 4.74. trimal