Updates to V-pipe's entry

[DrYak]

• in addition to share of N:

  • matcher is used for a pairwise alignment to the reference to asses low similarity.
  • smallgenomeutilities' frameshift_deletions_checks gives diagnostics about indels

• bcftools and smallgenomeutilities each have their own built-in routine for low coverage masking

• clearing confusion (sorry doc isn't very clear about this):

  • SAVAGE isn't used for denovo yet.
    (indeed a planned feature of V-pipe, but currently not yet in master)
  • ConsensusFixer and InDelFixer only post-processing tools for the consensus.
    Consensus itself is generated either by bcftools, smallgenomeutilities (for bwa or bowtie2 alignment)
    or as by-product of ngshmmalign alignment.

• latest commit ( 9f0ca4b6c989e38ea19a096f08edcaad58c009f0 - to be tagged as v2.99.2 by tomorrow)
  introduces BWA-based contaminant removal (option dehuman) before upload.
  We use it in production to publish on ENA.
  Not the typical use of contaminant removal (e.g.: before calling variants and consensus)
  but still worth noting.

• currently available as external scripts, to be integrated by the next version (2.99.3):

  • the iVar branch ( PR 113 ) is currently being merged into master.
  • our tool cojac is used in production to call mixture of lineages in wastewater environmental
    samples (see our cowwid repo), work is underway to integrate it into mainstream V-pipe.
  • external script is used in production to combine a CSV table reporting quality metrics
    that V-pipe computes. Work underway to integrate into mainstream V-pipe.

• general notes:

  • variant callers, haplotype engine and aligners are all user-selected.
  • V-pipe 2.0 has a benchmarking mode, it's currently being overhauled for V-pipe 3.0
  • it's an official Swiss Institute of Bioinformatics (SIB - the Elixir Swiss Node) Software resource,
    with long-term support:
    even as the PhDs will inevitably come and go as they finish their theses, there's a senior software
    developer attached to the project.

[DrYak]

latest commit ( 9f0ca4b6c989e38ea19a096f08edcaad58c009f0 - to be tagged as v2.99.2 by tomorrow)
introduces BWA-based contaminant removal (option dehuman) before upload.

tagged

[DrYak]

Sorry, completely forgot to update things, but primer trimming with either iVar or Samtools has been available in master in V-pipe for some time.