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. bams_multiqc
- 4.12. beast_gpu
- 4.13. classify_kaiju
- 4.14. classify_kraken2
- 4.15. classify_krakenuniq
- 4.16. classify_multi
- 4.17. classify_single
- 4.18. contigs
- 4.19. coverage_table
- 4.20. demux_metag
- 4.21. demux_only
- 4.22. demux_plus
- 4.23. deplete_only
- 4.24. diff_genome_sets
- 4.25. downsample
- 4.26. fastq_to_ubam
- 4.27. fetch_annotations
- 4.28. fetch_sra_to_bam
- 4.29. filter_classified_bam_to_taxa
- 4.30. filter_sequences
- 4.31. genbank
- 4.32. isnvs_merge_to_vcf
- 4.33. isnvs_one_sample
- 4.34. kraken2_build
- 4.35. mafft
- 4.36. mafft_and_snp
- 4.37. mafft_and_trim
- 4.38. merge_bams
- 4.39. merge_metagenomics
- 4.40. merge_tar_chunks
- 4.41. merge_vcfs
- 4.42. merge_vcfs_and_annotate
- 4.43. multiqc_only
- 4.44. scaffold_and_refine
- 4.45. subsample_by_metadata
- 4.46. subsample_by_metadata_with_focal
- 4.47. trimal