Nature Methods: doi: /nmeth Supplementary Figure 1. Ideograms showing scaffold boundaries and segmental duplication locations.

Transcription

1 Supplementary Figure 1 Ideograms showing scaffold boundaries and segmental duplication locations. Blue lines mark the boundaries of scaffolds. Black marks show the locations of segmental duplications. Magenta regions mark unassembled regions around the centromeres and telomeres. Ideogram were generated using The Genome Decoration Page, NCBI

2 Supplementary Figure 2 Architecture of complex regions at the MHC and Amylase loci. (a) MHC region (chr6: Mb). Upper panel: green bar = reference, blue bars = hybrid (bottom). Bottom panel: green phase blocks separated by SNVs in the hybrid in the middle. (b) Amylase region (chr1: Mb). Top panel: green bar = reference, blue bars = assemby. Assembly in the red box expanded to show nicking pattern in 450 kb region (bottom panel). (c) Haplotypes in increasing resolution to show alleles on the same phase block (green line = allele 1, grey line = allele 2).

3 Supplementary Figure 3 Assembly and phasing of Inversion. Inversion at Chr10q Mb with partial haplotyping.

4 Supplementary Table 1. Phasing comparisons. 10XG reads vs * 10XG reads vs hg19 Ref 21 vs Ref 21 vs hg19 Phased SNVs 2,783,119 2,615,312 2,421,740 2,221,354 Values removed 294, , , ,785 Phase block N Mb 16.7 Mb 145 kb 229 kb * Phasing data files are available at

5 Supplementary Table 2. Statistics for 10X-linked and hybrid assemblies built using different fragscaff parameters. In the third fragscaff processing stage, the score cutoff p was set to a range between 19 (the default auto-determined cutoff) and 150. The resulting assemblies were subsequently processed identically, as described in Materials and Methods. The with score cutoff of 36 (automatically determined using parameters j 1 and u 3) was chosen in this study as representing a middle ground with respect to accuracy, longest scaffold size, and overall contiguity. Score cutoff p19 (default) p36 (j1 u3) p50 p75 p100 p150 fragscaff Total contigs scaffolded Total scaffolds created Placement accuracy (%) Orientation accuracy (%) Bases properly placed (%) N50 (Mb) Assembly length (Gb) Longest scaffold (Mb) Number of scaffolds

6 Supplementary Table 3. Software tools used in this study and in related studies. Software/tool Task Settings Availability Reference / PMID SOAPdenovo Illumina short reads /soapdenovo.html Long Ranger (10X Genomics) BWA-MEM FragScaff Lastz Align to ref genome: evaluate accuracy and data visualization. Default Stage1: default Stage 2: default, -C = 10 Stage 3: Various combinations of j, u, and p (final: j=1, u=3, p=default) Accuracy evaluation: --nogapped -- notransition -- exact= identity=95 -- seed=match15 - -twins= ambiguous=n -- match=1,5 -- masking=3 Final alignment: RepeatMasker soft masking, -- format=sam -- nogapped -- notransition -- exact=500 maxwordcount= 90% -- identity=95 -- seed=match15 - -twins= s.com/downloads 10X barcode analysis and filtering, phasing Mapping 10X libraries to shortread-based 10X-linked scaffolding cts/fragscaff/files/ r_lab/dist/readme.lastz /README.lastz a.html n.github.io/ab yss-scaffoldpaper/

7 fragscaff_check Ordering.pl Knickers (BioNano Genomics) Irys Solve software (BioNano Genomics) Samtools Bedtools PhenoGram 10X Genomics Loupe evaluate fragscaff accuracy In silico nicking BioNano de-novo. Hybrid scaffold and genome maps alignment to reference maps File format conversion File format conversion Alignment visualization on ideograms Phasing, SNPs and SVs visualization ambiguous=n -- match=1,5 cts/fragscaff/files/ nickers/knickers.htm aining/docs/irysview_softw are_installation_guide_23. pdf net/ dtools2/releases ware/phenogramdownloads s.com/downloads