harmony

Compute error profiles from alignments.

Dependencies

• CCS
  • conda install -c bioconda pbccs
• Alignment
  • conda install -c bioconda pbmm2
• Harmony
  • Get binary from releases
  • DYI: boost, meson, ninja, C++20 compiler, Linux or MacOS environment
• Create plot
  • R with vroom, dplyr, ggplot2

How to compile (for dyi)

mkdir build && cd build
meson --prefix ~/mytools
ninja
ninja install

How to use

Generate HiFi data

ccs m64006_190824_131036.subreads.bam m64006_190824_131036.hifi.bam --log-level INFO

Align HiFi data

pbmm2 align --best-n 1 --preset HiFi \
            ref.fasta m64006_190824_131036.hifi.bam m64006_190824_131036.hifi.aligned.bam

Extract error profiles

harmony m64006_190824_131036.hifi.aligned.bam ref.fasta m64006_190824_131036

Plot curve

Provide one or more input files

scripts/single.R m64006_190824_131036 m64006_190827_133700

This generates a harmony.pdf similar to this example