Changes in Version 7.7

Major Changes

  • Changed iVar pipeline parameters: Minimum frequency threshold to call consensus was set 70% (-t 0.7).
  • Variant read frequency and total coverage at variant positions are shown for variants found in iVar pipeline.

 Minor Changes

  • New procedure statistics QC fields in iVar pipeline: Low frequency variants (genome wide), Variants (genome wide), Consensus Bases with Non-N Ambiguity.
  • Coverage plot can be inspected with Broad's Integrative Genomics Viewer (IGV) for read level QC.
  • New general procedure statistics field: GC-Content
  • Fixed storing of MST distance in stored comparison table retrievals

 

Changes in Version 7.6

  • New export function for sequences and metadata for batch-upload to GISAID.
  • New import function for sequences and metadata downloaded from GISAID.
  • New export of samples into a multiple FASTA file (e.g., for visualization with Nextclade).
  • Specific genome positions can be inspected with Broad's Integrative Genomics Viewer (IGV) for read level QC.
  • Changed iVar pipeline parameters: Samtools mpileup maximum depth (-k) set to 1,000,000 for better support of regions with high coverage (Parameter is changed automatically in existing pipeline scripts).
  • Changed SARS-CoV-2 database schema: Added 'Sampling Strategy', 'Nextstrain Clade', 'GISAID Clade', 'Ct Value'. Removed 'GISAID Download' tab fields and some 'Epi Characteristic' fields.
  • Replaced field 'Perc. Consensus Bases Below Coverage Threshold' with absolute value field 'Perc. Consensus Bases Below Coverage Threshold (Ns)'.
  • Allow offline installation of iVar on WSL.


Version 7.5

  • New SARS-CoV-2 Analysis with task templates for detection of notable mutations, PANGO lineage typing, and Illumina tiled amplicon pipeline.