README.md

AF-NS

Introduction

Workflow for identifying long-read novel sequences

Prerequisites

Make sure you have installed all of the following prerequisites on your machine：
• python2
• minimap2
• NUCmer
• porechop
• NanoFilt
• bedtools
• kraken2
• RepeatMasker

Run

python AF-NS.py -kraken_db db_folder -i input.fq -r ref.fa -o output_folder

kraken2 DB for human

We build kraken2 DB including archaea, bacteria, fungi, plasmid, viral and UniVec datasets, the link is as follows
http://www.bio8.cs.hku.hk/novel/kraken2_db.tar

output

Novel sequences: output_folder/novel.fa