NanoporeMapper

A simple command line tool to map nanopore reads with high accuracy

example call to download human ref genome

ncbi-genome-download -F fasta -t 9606 -R reference vertebrate_mammalian (c.f. https://github.com/kblin/ncbi-genome-download)

template script to chain some commands together

./mapper_wrapper.sh -d test1

This will:

1. Download specified reference genomes using the ncbi-genome-download package.
2. Create a magic-blast database of the collected reference genomes.