GDBr (pronounced Genome Debugger) is tool that identify Double-strand Break Repair (DSBR) using genome and variant. GDBr goes through three processes to identify DSBR. First step is preprocess the genome using RagTag and svim-asm and make sure they have same chromosome name with reference. Second step is correcting the variant using BLAST and filtering the variant which have repeat bt TRF and RepeatMasker, then save a csv file. Last step is to segregate the corrected variants into the appropriate DSBRs.
You need only reference sequence and query sequences file to use GDBr.
We strongly recommend using conda package manager to install GDBr.
conda create -n GDBr -c conda-forge -c bioconda -c chemical118 gdbr
conda activate GDBr
gdbr --versionAlso, you can use mamba package mamager to install GDBr quickly.
mamba create -n GDBr -c conda-forge -c bioconda -c chemical118 gdbr
mamba activate GDBr
gdbr --versiongdbr analysis -r <reference.fa> -q <query1.fa query2.fa ...> -s <species of data> -t <number of threads>The above command executes the following three processes simultaneously. If you want to redo some of the processes, you can manually run the command below.
By using RagTag and svim-asm, GDBr preprocess data and return properly scaffolded query .fa sequence file and variant .vcf file.
gdbr preprocess -r <reference.fa> -q <query1.fa query2.fa ...> -o prepro -t <number of threads>The preprocess step requires the use of a sorting program to do the scaffolding and variant calling, and even though they are allocated a lot of threads, they still don't use them all. An optimization approach is to distribute multiple queries to a small number of threads. However, this approach requires very high memory usage, so GDBr was developed to allow the user to freely choose this optimization by providing the --low_memory option.
By using BLAST, GDBr correct the variant file to analysis DSBR accurately. And, filter the repeat by using TRF, RepeatMasker.
gdbr correct -r <reference.fa> -q prepro/query/*.GDBr.preprocess.fa -v prepro/vcf/*.GDBr.preprocess.vcf -s <species of data> -o sv -t <number of threads>GDBr analysis the variant and identify DSBR mechanism.
gdbr analysis -r <reference.fa> -q prepro/query/*.GDBr.preprocess.fa -v sv/*.GDBr.correct.csv -o dsbr -t <number of threads>You can turn on different locus DSBR analysis by --diff_locus_dsbr_analysis, however analysis can give false positives due to partial homology on the sex chromosomes.
GDBr's final ouput is <query basename>.GDBr.result.tsv. This is simple description of the final output.
| Field | Description |
|---|---|
| ID | GDBr.<query order>.<variant order> |
| CALL_TYPE | Variant type : INS, DEL, etc |
| SV_TYPE | Corrected variant type : INS, DEL, SUB, etc |
| CHR | variant chromosome |
| REF_START | variant reference start location |
| REF_END | variant reference end location |
| QRY_START | variant query start location |
| QRY_END | variant query end location |
| GDBR_TYPE | GDBr variant type |
| HOM_LEN/HOM_START_LEN | INDEL : homology length / SUB : left homology length |
| HOM_END_LEN | SUB : right homology length |
| TEMP_INS_SEQ_LOC | templated insertion sequence location (REF or QRY) |
| DSBR_CHR | different locus DSBR chromosome |
| DSBR_START | different locus DSBR start |
| DSBR_END | different locus DSBR end |
| HOM_SEQ/HOM_START_SEQ | INDEL : homology sequence / SUB : left homology sequence |
| HOM_END_SEQ | SUB : right homology sequence |
| PUTATIVE_MECHANISM | GDBr DSB repair putative mechanism |
You can benchmark any command in GDBr with the --benchmark option by GNU time and psutil. It provides user time, system time, average CPU usage, multiprocessing efficiency, maximum RAM usage and wall clock time.
...
[2023-08-18 13:44:16] GDBr benchmark complete
User time (seconds) : 8007.44
System time (seconds) : 19901.00
Percent of CPU this job got : 7267%
Multiprocessing efficiency : 0.5118
Wall clock time (h:mm:ss or m:ss) : 6:23.99
Max memory usage (GB) : 23.5805