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_plot
- 4.3. assemble_denovo
- 4.4. assemble_refbased
- 4.5. bams_multiqc
- 4.6. beast_gpu
- 4.7. beast_to_auspice
- 4.8. build_augur_tree
- 4.9. classify_kaiju
- 4.10. classify_kraken2
- 4.11. classify_krakenuniq
- 4.12. classify_multi
- 4.13. contigs
- 4.14. coverage_table
- 4.15. demux_metag
- 4.16. demux_only
- 4.17. demux_plus
- 4.18. deplete_only
- 4.19. downsample
- 4.20. fastq_to_ubam
- 4.21. fetch_annotations
- 4.22. multi_Fetch_SRA_to_BAM
- 4.23. filter_classified_bam_to_taxa
- 4.24. genbank
- 4.25. isnvs_merge_to_vcf
- 4.26. isnvs_one_sample
- 4.27. kraken2_build
- 4.28. mafft
- 4.29. mafft_and_trim
- 4.30. merge_bams
- 4.31. merge_metagenomics
- 4.32. merge_tar_chunks
- 4.33. merge_vcfs
- 4.34. merge_vcfs_and_annotate
- 4.35. multiqc_only
- 4.36. newick_to_auspice
- 4.37. scaffold_and_refine
- 4.38. subsample_by_metadata
- 4.39. trimal