run.sh will produce .bam file using DAMAPPER.

This version of DAMAPPER supports 2 more options.

-o<temporary_directory>, -l<path_to_daligner>

I didn't touch the other parts. However, you can try this version with your own risk.

Prerequisites

1. DALIGNER : https://github.com/thegenemyers/DALIGNER
2. DAZZ_DB : https://github.com/thegenemyers/DAZZ_DB
3. LASTOOLS : https://github.com/gt1/lastools

Please install above packages.

Setup

1. Modify "configuration" part of run.sh according to your environment.
2. Make ref.dam from ref.fasta using fasta2DAM and DBsplit. You can refer this blog article.

Run

run.sh [ref.dam] [ref.fasta] [read.fasta] [out_dir]