stepStone v2.0

A pipeline for identification of chromothripsis breakpoints and cancer rearrangements

Download and Compile:

$ git clone  https://github.com/wtsi-hpag/stepStone.git 
$ cd stepStone 
$ bash install.sh

If everything compiled successfully you must see the final comment: "Congrats: installation successful!"

External packages

The genome aligner BWA-mem2 (https://github.com/bwa-mem2/bwa-mem2), minimap2 (https://github.com/lh3/minimap2) and samtools (http://www.htslib.org) are downloaded and compiled by stepStone.

Run the pipelines

Program: stepStone - a pipeline to identify chromothripsis breakpoints and rearrangements Version: 2.0

Usage: ./stepStone command [options] \

Commands:
-- breakpoints Detect breakpoints
-- plot Plot depth of coverage
-- align Align reads to a reference \

===Detect breakpoints with aligned, and name sorted sam,bam or cram files: \

       $ /full/path/to/stepStone/src/stepStone breakpoint -nodes 60        \
	-data ccs/ont/ont-NLR/ngs-HiC/ngs-10X/ngs-SSR                  \
	-bam /myspace/desk/test-sorted.bam <output_breakpoints.vcf>    \
	--- Note: the sam/bam/cram file has to be Name sorted! ---     \
	--- If not read name sorted, please do the following:  ---     \
	--- samtools sort -@ 60 -n your.bam new.bam ---                \

===Detect breakpoints with fasta/fastq long read files: \

       $ /full/path/to/stepStone/src/stepStone breakpoint -nodes 60 -data ccs/ont 	\
	-reads input_long.fasta/q <Input_Reference> <breakpoints.vcf>  		\

===Plot depth of coverage for all data types: \

       $ /full/path/to/stepStone/src/stepStone plot -bam /myspace/test-sorted.bam -sample cancer \

===Align reads to a reference for all data types: \

       $ /full/path/to/stepStone/src/stepStone align -data ccs/ont/ont-NLR 			\
	-reads input_long.fasta/q <Input_Reference> <Output_sorted_bam>			\

       $ /full/path/to/stepStone/src/stepStone align -data ngs-HiC         			\
	-fq1 read_1.fq.gz -fg2 read_2.fq.gz <Input_Reference> <Output_sorted_bam>  	\

       $ /full/path/to/stepStone/src/stepStone align -data ngs-10X                     	\
	-fq1 read_1.fq.gz -fg2 read_2.fq.gz <Input_Reference> <Output_sorted_bam>  	\

       $ /full/path/to/stepStone/src/stepStone align -data ngs-SSR                     	\
	-fq1 read_1.fq.gz -fg2 read_2.fq.gz <Input_Reference> <Output_sorted_bam>  	\

	-nodes     60     - Number of CPUs requested                 			\
	-data     ccs     - PacBio Hifi                 				\
	-data     ont     - Oxford Nanopore Q20 or Q30                 			\
	-data     ont-NLR - Oxford Nanopore normal long reads (NLR)    			\
	-data     ngs-HiC - Hi-C reads                                 			\
	-data     ngs-10X - 10X reads                                 			\
	-data     ngs-SSR - Standard short reads such as Illumina data 			\


       $ /full/path/to/stepStone/src/stepStone -nodes <nodes>  \