Blackbird: Tool for SV detection with Synthetic Long Reads (SLR) and hybrid (SLR+Long reads datasets)
Blackbird 0.1 Manual
Blackbird is a novel integrated alignment- and local-assembly-based algorithm hat employs the barcode information encoded in SLR reads to improve detection and placement of challenging medium-size events (50-10,000bp). Blackbird assembles the genome into segments and calls insertions and deletions in these segments. Without the need for a computationally expensive whole genome assembly, Blackbird uses a barcode-aware sliding window approach to assemble small segments of the target genome and sensitively call SVs in these segments.
Blackbird is able to work with SLR read datasets and a combination of SLR read and long-read datasets. We evaluated our method on both simulated and real whole genome human datasets. In a SLR read mode Blackbird outperforms existing short-read and SLR read methods, especially for insertions. In a hybrid-mode Blackbird demonstrated results similar to state-of-the-art long read tools, but requires less long reads to achieve same results. Therefore, our method might decrease the cost of SV calling in clinical setting, without losing in the result quality.
Initially Blackbird was forked from the SPAdes reposotory and have a common codebase. To compile Blackbird in assembler foder execute:
./spades_compile.sh
Blackbird binary can be found inside bin folder. Additionally, you should install and compile SPAdes for blackbird.
--bam or -b [required] - position-sorted and indexed SLR Read bam-file with BX tags
--rerefence or -r [required] - BWA-indexed reference genome
--output or -o [required] - Folder where results will be stored
--spades or -s - Path to spades.py from spades_for_blackbird repository (not needed if spades.py is in path)
--long-bam or -l - Position-sorted and indexed long read file (optional, should be paired with long-read option)
--long-read or -m - FASTQ-file with the same long reads (optional, should be paired with long-bam option)
--threads or -t - Number of threads (default is 1, but more threads is beneficial)
--regions or -r [optional] - File with regions where SV should be called. Each row in the file is space-separated and has "chr start end" format
--help or -h - Print this message
Hidden options
-d - Don't delete assembly folders. It allows to inspect contigs that were used for SV calling
-n - Don't collect poorly aligned reads
All files are stored in the output folder which is set by the user.
out_50.vcf is a position sorted VCF file, that contains insertion and deletion calls longer than 50 bp.
out.vcf contains all other calls, though they are not reliable.
/home/dmm2017/Blackbird/assembler/bin/blackbird -b /local/storage/data/10X/HG002/NA24385.GRCh37.phased_possorted_bam.bam -r /local/workdir/dmm2017/hg37/refdata-hg19-2.1.0/fast a/genome.fa -o blackbird_10X_chr1 -g genome.txt -t 32 -s /home/dmm2017/spades_for_blackbird/assembler/spades.py
Blackbird is not published yet, but it is selected for presentation at Genome Informatics 2022.
Feel free to drop any inquiry to meleshko.dmitrii@gmail.com