Evaluating the impact of assemblers, aligners, sequencer and read length on read-based and assembly-based SV detection.
The major parts involved in the comparison are listed below:
- Using six long read datasets (details), we assessed the impact of dataset, aligner and assembler on the detection variability.
- On each dataset, 20 read-based callsets and four assembly-based callsets were compared to assess the impact of aligner and assembler.
- Based on the analysis of 2, we build high-confident insertions and deletions (insdel) callsets of read and assembly. The high-confident insdel callsets are then compared.
- Benchmarking 20 read-based and eight assembly-based detection piplines with well curate SVs of HG002 released by GIAB.
Please check the wiki page for more details about SV detection and benchmarking.
NOTE: The raw VCF files of all callers among six datasets are available for reproducing the figures (reproduce_data).
## Tools
Jasmine=1.1.4
Samtools=1.9
## Python packages
python=3.6
pandas=1.1.5
numpy=1.19.5
seaborn=0.11.1
pysam=0.15.3
matplotlib_venn=0.11.7
intervaltree=3.1.0
## Create a python environment
conda create -n py36 python=3.6
conda activate py36
## Install required packages
pip install seaborn==0.11.1
pip install matplotlib-venn==0.11.9
pip install pysam==0.15.3
pip install intervaltree==3.1.0
## Install Jasmine
conda config --add channels bioconda
conda config --add channels conda-forge
conda install jasminesv
Hg19 reference genome hs37d5.fa.
Please refer CAMPHOR for the process of original repeat files. The files listed below will be used in the analysis (download hg19_repeats and unzip).
- Simple repeat file including STR and VNTR (simplerepeat.bed.gz).
- Segmental duplication file (seg_dup.bed.gz).
- Repeat masker file including LINE, SINE and etc (rmsk.bed.gz).
- Hg19 excluded regions (grch37.exclude_regions_cen.bed).
NOTE: Unzip reproduce_data.zip, and the default work directory is ./reproduce_data/.
Then, the following variables should be specified in ./Helpers/Constant.py.
WORKDIR = '/path/to/reproduce_data'
FIGDIR = '/path/to/reproduce_data/Figures'
HG19REF = '/path/to/hs37d5.fa'
EXREGIONS = '/path/to/hg19_repeats/grch37.exclude_regions_cen.bed'
SIMREP = '/path/to/hg19_repeats/simplerepeat.bed.gz'
RMSK = '/path/to/hg19_repeats/rmsk.bed.gz'
SD = '/path/to/hg19_repeats/seg_dup.bed.gz'
SAMTOOLS = '/path/to/samtools'
JASMINE = '/path/to/jasmine'
NOTE: Please run the scripts by the order listed below.
## Figure 2a
python ./Figure2/Figure2a.py
## Figure 2b and 2c
python ./Figure2/Figure2bc.py
## Figure 2d, 2e, 2f and 2g
python ./Figure2/Figure2defg.py
## Figure 3a, 3b and 3c
python ./Figure3/Figure3abc.py
## Figure 3d, 3e and 3f
python ./Figure3/Figure3def.py
## Figure 4a, 4b, 4c and 4d
python ./Figure4/Figure4.py
## Figure 5a, 5b, 5c, 5d, 5e and 5f
python ./Figure5/Figure5.py
## Extended Data Fig 1
python ./SuppFig/FigS1.py
## Extended Data Fig 2
python ./SuppFig/FigS2.py
## Extended Data Fig 3
python ./SuppFig/FigS3.py
## Extended Data Fig 4
python ./SuppFig/FigS4.py
## Extended Data Fig 5
python ./SuppFig/FigS5.py
## Extended Data Fig 6
python ./SuppFig/FigS6.py
## Extended Data Fig 7
python ./SuppFig/FigS7.py