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