/harmony

Compute error profiles from alignments

Primary LanguageC++BSD 3-Clause Clear LicenseBSD-3-Clause-Clear

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++14 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

~/mytools/bin/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