Sample input data for running snakefile:
-- raw reads -- http://www-rcf.usc.edu/~mchaisso/hgsvg/phase2/lra/HG00514.PacBioSequel2.EDEVI_20190208_S64018_PL100119428-1_B01.subreads.bam.sorted.lra.bam http://www-rcf.usc.edu/~mchaisso/hgsvg/phase2/pbmm2/HG00514.PacBioSequel2.EDEVI_20190208_S64018_PL100119428-1_B01.subreads.bam.sorted.bam
-- assemblies -- http://www-rcf.usc.edu/~mchaisso/hgsvg/phase2/cov-30/HG00514.SequelII.CLR.30x.haplotype1.fa http://www-rcf.usc.edu/~mchaisso/hgsvg/phase2/cov-30/HG00514.SequelII.CLR.30x.haplotype2.fa http://www-rcf.usc.edu/~mchaisso/hgsvg/phase2/cov-40/HG00514.SequelII.CLR.40x.haplotype1.fa http://www-rcf.usc.edu/~mchaisso/hgsvg/phase2/cov-40/HG00514.SequelII.CLR.40x.haplotype2.fa http://www-rcf.usc.edu/~mchaisso/hgsvg/phase2/cov-50/HG00514.SequelII.CLR.50x.haplotype1.fa http://www-rcf.usc.edu/~mchaisso/hgsvg/phase2/cov-50/HG00514.SequelII.CLR.50x.haplotype2.fa http://www-rcf.usc.edu/~mchaisso/hgsvg/phase2/cov-75/HG00514.SequelII.CLR.75x.haplotype1.fa http://www-rcf.usc.edu/~mchaisso/hgsvg/phase2/cov-75/HG00514.SequelII.CLR.75x.haplotype2.fa http://www-rcf.usc.edu/~mchaisso/hgsvg/phase2/ccs-1/assembly.1.consensus.fasta http://www-rcf.usc.edu/~mchaisso/hgsvg/phase2/ccs-1/assembly.2.consensus.fasta http://www-rcf.usc.edu/~mchaisso/hgsvg/phase2/ctg-1/assembly.1.consensus.fasta http://www-rcf.usc.edu/~mchaisso/hgsvg/phase2/ctg-1/assembly.2.consensus.fasta http://www-rcf.usc.edu/~mchaisso/hgsvg/phase2/flye2/assembly.1.fasta http://www-rcf.usc.edu/~mchaisso/hgsvg/phase2/flye2/assembly.2.fasta http://www-rcf.usc.edu/~mchaisso/hgsvg/phase2/tworuns/assembly.1.consensus.fasta http://www-rcf.usc.edu/~mchaisso/hgsvg/phase2/tworuns/assembly.2.consensus.fasta
-- SV calls with support -- http://www-rcf.usc.edu/~mchaisso/hgsvg/phase2/all_support.tgz