checkV-

[mult1fractal]

• CheckV

• fully automated command-line pipeline for assessing the quality of metagenome-assembled viral genomes, including identification of host contamination for integrated proviruses, estimating completeness for genome fragments, and identification of closed genomes.

• working commands:

  checkv completeness T7_draft/phage_positive_contigs/T7_draft_positive_contigs.fa -d ../DB/checkv-db-v0.6 -t 30 results
  checkv repeats T7_draft/phage_positive_contigs/T7_draft_positive_contigs.fa  results
  checkv contamination T7_draft/phage_positive_contigs/T7_draft_positive_contigs.fa -d ../DB/checkv-db-v0.6 -t 30 results

• based on three commands above: generates summary file

  quality_summary T7_draft/phage_positive_contigs/T7_draft_positive_contigs.fa  results

Output:

contig_id contig_length genome_copies gene_count viral_genes host_genes checkv_quality miuvig_quality completeness completeness_method contamination prophage termini
ctg1_len=102949 102949 1.01 161 109 0 High-quality High-quality 100.0 AAI-based 0.0 No NA
ctg2_len=44018 44018 1.0 70 11 0 Not-determined Genome-fragment NA NA 0.0 No NA
ctg3_len=25734 25734 1.0 55 27 0 Not-determined Genome-fragment NA NA 0.0 No NA
ctg4_len=21924 21924 1.0 24 8 0 Not-determined Genome-fragment NA NA 0.0 No NA
ctg5_len=16494 16494 1.0 10 0 0 Not-determined Genome-fragment NA NA 0.0 No NA
ctg6_len=5303 5303 1.0 5 2 0 Not-determined Genome-fragment NA NA 0.0 No NA

• extend with tools e.g. virnet hit yes/no

• extend table via .join (channelhandling training) --- .join Taxonomic classification from sourmash

• --> nice overview table :)

• possible pro phage tool?

• should be rdy for Release -r v0.7

[replikation]

nanozoo/checkv:0.4.0--f3ed06e

[replikation]

• implemented