How-to-guides

The how-to-guides below give a more thorough discussion on several problems users may face while using floria.

• Guide: how to generate a good .vcf and .bam file for phasing
  • Alignment: Use-case 1 - metagenomic contig phasing
    • Metagenome-assembled genomes?
  • Alignment: Use-case 2 - reference-based phasing
    • Making sure your reference genomes are comprehensive (metagenomics)
  • Variant calling: using a good low-frequency SNP caller
    • Short reads
    • Long reads
• Guide: optimizing parameters for phasing
  • Error rate -e
  • Block length -l
  • Beam search number of solutions -n
  • Ploidy sensitivity -s
  • –no-stop-heuristic
  • –ignore-monomorphic
• Guide: understanding output phasings and their pitfalls
  • TLDR
  • How many strains are there in my contig?
  • Spurious variants cause high “strain count”
  • Species cross mappings cause high “ploidy”
  • Short reads give smaller contig multiplicity
  • Number of strains is more accurate when the coverage is higher
  • and remember, visualization is important!