SVDSS
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Parsoa
Improved structural variant discovery in accurate long reads using sample-specific strings (SFS)
Dear author, Firstly, I got 22 ```sfs``` files after running ```SVDSS search --index ./hg38.fmd --workdir ./HG00733/ --bam HG00733/smoothed.selective.bam```. Each of the ```sfs`` file is named as ```solution_batch_*.sfs``` and contains some...
Hello, Thank you for developing this tool. I'm using SVDSS search to extract SFS from two assembled contig genomes. The documentation mentions support for FASTA Extract SFS, Extract SFS from...
Hi Sorry for submitting a bunch of new issues at a time. I'm kind of curious about the running time SVDSS needed to index and search on datasets with different...
Hi, Thank you for developing this amazing tool. Recently, I've tried to use SVDSS to find SFSs between two assemblies (or an assembly and the reference genome), however, SVDSS failed...
Thank you for providing the excellent tool. I tried to use HG002 HiFi and ONT long reads for running SVDSS. Although SVDSS output a complete set of SVs when using...
"It requires as input the BAM file of the sample to be genotyped.” In this step: "SVDSS smooth --bam sample.bam --workdir $PWD --reference GRCh38.fa --threads 16", My understanding is that...
Hello, I wonder if the method to detect SFS strings could be applied to other highly accurate datasets such as unitigs created from Illumina reads (e.g. PE, 2x150 bp, 500...
Hi, I was trying to use this exciting tool to call SVs using HiFi reads on a genome assembled from those same reads. I can run `SVDSS index` and `SVDSS...
I am running into seg fault while running "smooth" similar to https://github.com/Parsoa/SVDSS/issues/12. I have installed SVDSS through conda and also checked using binary distribution. In both cases, same result (Seg...
Hi, I am trying to use SVDSS, but it seems that it is not working for me. ``` refgen=//data/humans/GRCh38_latest_genomic.fna.gz SVDSS index --threads 50 --fastq $refgen --index refgen.bwt & SVDSS smooth...
