conda install AquilaSV

(Please ensure channels are properly setup for bioconda before installing)

AquilaSV_step1 --help
AquilaSV_step2 --help
AquilaSV_step3 --help

AquilaSV utilizes Python3 (+ numpy, pysam, sortedcontainers, and scipy), SAMtools, and minimap2. To be able to execute the above programs by typing their name on the command line, the program executables must be in one of the directories listed in the PATH environment variable (".bashrc").
Or you could just run "./install.sh" to check their availability and install them if not, but make sure you have installed "python3", "conda" and "wget" first.

git clone https://github.com/maiziex/AquilaSV.git
cd AquilaSV
chmod +x install.sh
./install.sh

After running "./install.sh", a folder "source" would be download.

Put the "AquilaSV/bin" in the ".bashrc" file, and source the ".bashrc" file
Or just use the fullpath of "AquilaSV_step1.py", "AquilaSV_step2.py" and "AquilaSV_step3.py"

*We provide a test example dataset to run the whole pipeline.

python3 AquilaSV/bin/AquilaSV_step1.py  --bam_file selected.bam --vcf_file test_freebayes.vcf --chr_num 3 --out_dir test_sv

--bam_file: "selected.bam" is a bam file generated from BWA-MEM/LongRanger/EMA and samtools. How to get the bam file, you can also check here.

--vcf_file: "test_freebayes.vcf" is a VCF file generated from variant caller like "FreeBayes". How to get the vcf file, you can also check here.

--chr_num: "3" is the chromosome number you need to define for the target region or the structural variant you are interested in.

--mole_boundary: default = 50000 (50kb). We use 50kb to differentiate reads with the same barcode are drawn from different long molecules.

--out_dir: default = ./AquilaSV_results. You can define your own folder name.

--num_threads: default = 8.

--num_threads_bwa_mem: number of threads for bwa-mem, default = 20

--clean: default = 1. It will delete all assembly files from SPAdes and intermediate bam/fastq files from AquilaSV.

python3 AquilaSV/bin/AquilaSV_step2.py --out_dir test_sv --chr_num 3 --reference genome_hg19.fa

--chr_num: "3" is the chromosome number you need to define for the target region or the structural variant you are interested in.

--reference: "genome_hg19.fa" is the human reference fasta file.

--out_dir: default = ./AquilaSV_results, make sure it's the same as "--out_dir" from Step1 if you want to define your own output directory name.

--num_threads: default = 10, this determines the number of files assembled simultaneously by SPAdes.

--num_threads_spades: default = 5, this is the "-t" for SPAdes.

python3 AquilaSV/bin/AquilaSV_step3.py  --assembly_dir test_sv  --ref_file genome_hg19.fa  --chr_num 3 

--assembly_dir: folder to store assembly results from step1 and step2 (same as "--out_dir" for step1 and step2).

--ref_file: "genome_hg19.fa" is the human reference fasta file.

--chr_num: "3" is the chromosome number you need to define for the target region or the structural variant you are interested in.

--out_dir: default = ./AquilaSV_Step3_Results. Directory to store the final VCF file from AquilaSV, and you can define your own folder name

--var_size: default = 1, variant size, cut off size for indel and SV,

--num_of_threads: number of threads, default = 1

--clean: default = 1. You can choose to delete diate files or no

test_sv/AquilaSV_step3_results: Aquila_contig_final.vcf

test_sv
|
|-H5_for_molecules 
|   └-target_chr3_sorted.h5    --> (molecule files for target region including barcode, variants annotation (0: ref allele; 1: alt allele), coordinates for each molecule)
|
|-results_phased_probmodel
|   └-chr*.phased_final        --> (Phased molecule files)
|
|
|-Local_Assembly_by_chunks
|   └-chr*_files_cutPBHC
|       |-fastq_by_*_*_hp1.fastq                  --> (reads fastq file for haplotype 1)
|       |-fastq_by_*_*_hp2.fastq                  --> (reads fastq file for haplotype 2)
|       
|
|-Assembly_Contigs_files
|    |-Aquila_Contig_chr*.fasta                    --> (final contigs fasta file for the target region)
|    |-Aquila_Contig_chr*.bam                      --> (final contigs bam file for the target region)
|    |-Aquila_Contig_chr*_hp1.fasta                     --> (final contigs fasta file for haplotype 1)
|    └-Aquila_Contig_chr*_hp2.fasta                     --> (final contigs fasta file for haplotype 2)
|
└-AquilaSV_step3_results
     └-AquilaSV_Contig_final.vcf --> (final VCF including SNPs, small Indels and SVs)