## # varRep ## track rmsk shortLabel RepeatMasker longLabel Repeating Elements by RepeatMasker group varRep visibility hide itemRgb on type bigBed 9 + bigDataUrl rmsk.bigBed maxWindowToDraw 10000000 priority 1 track simpleRepeat shortLabel Simple Repeats longLabel Simple Tandem Repeats by TRF group varRep visibility hide type bigBed 4 + bigDataUrl simpleRepeat.bb priority 2 track as_annotation shortLabel AS annotation longLabel Alpha satellite annotation group varRep visibility hide type bigBed 9 itemRgb on bigDataUrl as_annotation.bigBed maxItems 100000 priority 3 track hor_decompositions shortLabel HOR annotation longLabel Centromere HOR annotation group varRep visibility hide itemRgb on type bigBed 9 bigDataUrl hor_decompositions.bigBed maxItems 100000 priority 4 track segdups shortLabel Segmental Dups longLabel Segmental Duplications group varRep visibility hide itemRgb on type bigBed 9 bigDataUrl segdups/segdups.bigBed priority 5 track segdupslow shortLabel Segmental Dups Low Id longLabel Segmental Duplications Low Identity group varRep visibility hide itemRgb on type bigBed 9 bigDataUrl segdups/segdupslow.bigBed priority 7 html segdups.html track dupmasker shortLabel Ancestral Seg Dups longLabel Ancestral segmental duplications by DupMasker group varRep visibility hide itemRgb on type bigBed 9 bigDataUrl dupmasker.bigBed priority 8 # track merqury # shortLabel Merqury # longLabel Merqury # superTrack on hide # visibility hide # group map # priority 10 track merqury_10X_reads_kmers #parent merqury shortLabel Merqury 10XG k-mers longLabel Merqury k-mer multiplicity in 10XG reads type bigWig 0.0 100.0 color 60,60,140 altColor 140,60,60 visibility hide bigDataUrl merqury/merqury_10X_reads_kmers.bigWig viewLimitsMax 0:100 maxHeightPixels 100:32:8 priority 1 group map track merqury_assembly_kmers #parent merqury shortLabel Merqury assembly k-mers longLabel Merqury k-mer multiplicity in assembly color 60,60,140 altColor 140,60,60 type bigWig 0.0 100.0 visibility hide bigDataUrl merqury/merqury_assembly_kmers.bigWig viewLimitsMax 0:100 maxHeightPixels 100:32:8 priority 2 group map track merqury_marker_kmers #parent merqury shortLabel Merqury marker k-mers longLabel Merqury Single copy marker k-mers color 60,60,140 altColor 140,60,60 type bigWig 0.0 100.0 visibility hide bigDataUrl merqury/merqury_marker_kmers.bigWig viewLimitsMax 0:100 maxHeightPixels 100:32:8 priority 3 group map track merqury_errors #parent merqury shortLabel Merqury errors longLabel Merqury - Assembly-only (Errors) color 60,60,140 altColor 140,60,60 type bigWig 0.0 100.0 visibility hide bigDataUrl merqury/merqury_errors.bigWig viewLimitsMax 0:100 maxHeightPixels 100:32:8 priority 4 group map # track winnowmap_nanopore # shortLabel Winnowmap Nanopore SVs # longLabel Winnowmap Nanopore SVs # superTrack on hide # visibility hide # group map # priority 10 track winnowmap_nanopore_aligns #parent winnowmap_nanopore shortLabel Winnowmap Nanopore Alignments longLabel Winnowmap Nanopore Alignments priority 10 type bam maxItems 1000000 visibility hide bigDataUrl winnowmap_nanopore/winnowmap_nanopore_aligns.bam group map track winnowmap_nanopore_variants #parent winnowmap_nanopore shortLabel Winnowmap Nanopore Variants longLabel Winnowmap Nanopore Variants type vcfTabix maxWindowToDraw 200000 bigDataUrl winnowmap_nanopore/winnowmap_nanopore_variants.vcf.gz priority 20 visibility hide group map # track hg002_aligns # shortLabel HG002 to CHM13 alignments # longLabel HG002 to CHM13 alignments # superTrack on hide # visibility hide # group compGeno # priority 10 track HG002vCHM13_20200602_mm2_ONT #parent hg002_aligns shortLabel HG002 ONT minimap2 longLabel HG002 ONT minimap2 alignments priority 10 type bam maxItems 1000000 visibility hide bigDataUrl HG002vCHM13/HG002vCHM13_20200602_mm2_ONT.sort.bam group compGeno track HG002vCHM13_20200602_mm2_PBCCS #parent hg002_aligns shortLabel HG002 PacBio HiFi minimap2 longLabel HG002 PacBio HiFi minimap2 alignments priority 11 type bam maxItems 1000000 visibility hide bigDataUrl HG002vCHM13/HG002vCHM13_20200602_mm2_PBCCS.sort.bam group compGeno track HG002vCHM13_20200602_mm2_PB #parent hg002_aligns shortLabel HG002 PacBio CLR minimap2 longLabel HG002 PacBio CLR minimap2 alignments priority 12 type bam maxItems 1000000 visibility hide bigDataUrl HG002vCHM13/HG002vCHM13_20200602_mm2_PB.sort.bam group compGeno track HG002vCHM13_20200602_ngmlr_PBCCS #parent hg002_aligns shortLabel HG002 PacBio HiFi NGMLR longLabel HG002 PacBio HiFi NGMLR alignments priority 13 type bam maxItems 1000000 visibility hide bigDataUrl HG002vCHM13/HG002vCHM13_20200602_ngmlr_PBCCS.sort.bam group compGeno track HG002vCHM13_20200602_ngmlr_PB #parent hg002_aligns shortLabel HG002 PacBio CLR NGMLR longLabel HG002 PacBio CLR NGMLR alignments priority 14 type bam maxItems 1000000 visibility hide bigDataUrl HG002vCHM13/HG002vCHM13_20200602_ngmlr_PB.sort.bam group compGeno