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gaap's Introduction

GAAP

A genome assembly assessment pipeline.

Introduction

GAAP is a pipeline to assess genome assembly.

Installation

Dependencies

Base accuracy (mapping)

  • bwa v0.7.17-r1198-dirty
  • samtools v1.9
  • bcftools v1.9

Base accuracy (k-mer)

  • meryl v1.3
  • merqury v1.3

breakpoint detection

  • Bio::DB::Sam v1.43 (perl module)
  • minimap2 v2.17-r974-dirty
  • samtools v1.9

busco

  • Augustus (> 3.2.1)
  • blastn
  • hmmer v3.1b2

SNV-depth dot plot

  • minimap2 v1.9 (for TGS reads mapping). Can be install by conda with command "conda install perl-bio-samtools -c bioconda".
  • bwa v0.7.17-r1198-dirty (for NGS reads mapping)
  • Rscript v4.0.3 (for plotting)
  • ggplot2 (R module)
  • ggExtra (R module)

Usage

GAAP

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