viral-ngs: genomic analysis pipelines for viral sequencing¶
Contents¶
- 1. Description of the methods
- 2. Using the WDL pipelines
- 3. WDL Workflows
- 3.1. align_and_count_report
- 3.2. align_and_plot
- 3.3. assemble_denovo
- 3.4. assemble_denovo_with_deplete
- 3.5. assemble_denovo_with_deplete_and_isnv_calling
- 3.6. assemble_denovo_with_isnv_calling
- 3.7. assemble_refbased
- 3.8. bams_multiqc
- 3.9. build_augur_tree
- 3.10. classify_kaiju
- 3.11. classify_krakenuniq
- 3.12. contigs
- 3.13. coverage_table
- 3.14. demux_metag
- 3.15. demux_only
- 3.16. demux_plus
- 3.17. deplete_only
- 3.18. downsample
- 3.19. fetch_annotations
- 3.20. multi_Fetch_SRA_to_BAM
- 3.21. filter_classified_bam_to_taxa
- 3.22. genbank
- 3.23. isnvs_merge_to_vcf
- 3.24. isnvs_one_sample
- 3.25. mafft
- 3.26. mafft_and_trim
- 3.27. merge_bams
- 3.28. merge_tar_chunks
- 3.29. multiqc_only
- 3.30. scaffold_and_refine
- 3.31. trimal