Author: Peng Xu
Email: pxu@uabmc.edu
Draft date: Sep. 8, 2019
CCSkit was developed to comprehensively characterize genomic mutations (SNPs, Indels, Structural variations) from CCS long reads.
The program was tested on a x86_64 Linux system with 12 cores, each with a 4GB physical memory. The work can be usually finished within an hour for a 60x CCS long read sample.
Dependency: Python3, samtools should be installed in current path.
git clone git@github.com:penguab/CCSkit.git
Then, please also add this directory to your PATH:
export PATH=$PWD/CCSkit/:$PATH
CCSkit needs two files as inputs. The first is a bam file from CCS long read alignment. The second is the genome reference (FASTA format).
python CCSkit.py -b <bam file> -g <genome.fa>
9/8/2019: First version released.