ontbc

Pipeline for oxford nanopore barcoding

1. Dependence

python 2.5 or higher
porechop (optional, barcode required)
SGE (optional)

2. Install

git clone https://github.com/FlyPythons/ontbc.git
cd ontbc
chmod 755 ontbc.py

3. Usage

3.1 clean raw reads

raw ont fastq made by oxford nanopore ctd. has many errors, so we should clean the fastq before downstream analysis

ontbc.py clean input.fastq > clean.fastq

3.2 filter raw reads

use to filter ont reads with read_length and read_quality_score

ontbc.py filter --fastq 1.fastq --summary 1.summary.txt \
--min_score 7 --min_length 1000 

3.3 barcoding

use to ont reads barcoding

ontbc.py barcode /path/to/cell/ --barcode BC01 BC02 BC03