Journal: G3: Genes|Genomes|Genetics

Article Title: Reference genomes for BALB/c Nude and NOD/SCID mouse models

doi: 10.1093/g3journal/jkad188

Figure Lengend Snippet: Basic genome assembly statistics.

Article Snippet: To further improve the continuity of the assembled HIFI contigs, we used Bionano optical maps as anchors for scaffolding.

Techniques:

Journal: G3: Genes|Genomes|Genetics

Article Title: Reference genomes for BALB/c Nude and NOD/SCID mouse models

doi: 10.1093/g3journal/jkad188

Figure Lengend Snippet: Identification of reference features that are absent in BALB/c Nude and NOD/SCID mice. a) Circular visualization of annotated reference features that could not be identified in the genome assemblies of BALB/c Nude and NOD/SCID strains. The organization of chromosomes is similar to that in , except that the slices representing the 5 chromosomes with most number of missing protein-coding features were enlarged for clarity. Color codes indicate types of features. b) Close-up view of the highlighted region containing members of the defensin alpha cluster on chromosome 8 (21,859,396-21,942,429; GRCm39). HIFI reads of one representative NOD/SCID (sample 3, upper panel) and BALB/c Nude (sample 6, lower panel) individual aligned to GRCm39 genome using minimap2 and visualized in IGV (Integrative Genomics Viewer) browser in upper and lower panels, respectively. Mismatch coloring was deactivated for clarity.

Article Snippet: To further improve the continuity of the assembled HIFI contigs, we used Bionano optical maps as anchors for scaffolding.

Techniques:

Journal: G3: Genes|Genomes|Genetics

Article Title: Reference genomes for BALB/c Nude and NOD/SCID mouse models

doi: 10.1093/g3journal/jkad188

Figure Lengend Snippet: Identification of reference features that are specifically absent in BALB/c Nude strain. a) GRCm39 features that are absent specifically in BALB/c Nude genome assembly were plotted similarly to that in . b) Close-up view of Klra genes region on chromosome 6 (129,982,946-130,193,356; GRCm39). HIFI reads of one representative NOD/SCID (sample 3, upper panel) and BALB/c Nude (sample 6, lower panel) individual were aligned to GRCm39 genome using minimap2 and visualized similarly to that in .

Article Snippet: To further improve the continuity of the assembled HIFI contigs, we used Bionano optical maps as anchors for scaffolding.

Techniques:

Journal: Frontiers in Plant Science

Article Title: Representing true plant genomes: haplotype-resolved hybrid pepper genome with trio-binning

doi: 10.3389/fpls.2023.1184112

Figure Lengend Snippet: Experimental assembly comparison.

Article Snippet: Step 4 scaffolded the assemblies to the corresponding Bionano contig-assembly hybrid scaffolds using Ragtag ‘scaffold’.

Techniques: Comparison, Software

Journal: Frontiers in Plant Science

Article Title: Representing true plant genomes: haplotype-resolved hybrid pepper genome with trio-binning

doi: 10.3389/fpls.2023.1184112

Figure Lengend Snippet: Haplotype switching. Haplotype switching was illustrated by aligning TrioCanu binned HiFi reads of parent A (HDA149) and parent B (HDA330) to each contig level genome assembly. The x-axis shows 1 Mb windows across contigs. The contigs were arranged from longest to shortest. Vertical gray lines show the boundaries of contigs. The y-axis shows the difference in percent coverage of the binned reads over a 1 Mb window of the given assembly. Higher coverage of HDA149 is shown in pink and higher coverage of HDA330 is shown in blue. (A) Hifiasm HDA149 assembly with trio-binning. (B) Hifiasm HDA330 assembly with trio-binning. (C) TrioCanu HDA149 assembly with trio-binning. (D) TrioCanu HDA330 assembly with trio-binning. (E) Hifiasm haplotype 1 assembly in default run mode, without parental k-mers for trio-binning. (F) Hifiasm haplotype 2 assembly in default run mode, without parental k-mers for trio-binning.

Article Snippet: Step 4 scaffolded the assemblies to the corresponding Bionano contig-assembly hybrid scaffolds using Ragtag ‘scaffold’.

Techniques:

Journal: The Plant Cell

Article Title: Is It Ordered Correctly? Validating Genome Assemblies by Optical Mapping ^[OPEN]

doi: 10.1105/tpc.17.00514

Figure Lengend Snippet: Recent Results of Physical Maps Aligned to Their Respective Reference Genomes

Article Snippet: Bionano contigs are illustrated as cyan bars with a light blue coverage plot and many dark blue vertical BssSI matches to the genome sequence.

Techniques: Sequencing

Journal: The Plant Cell

Article Title: Is It Ordered Correctly? Validating Genome Assemblies by Optical Mapping ^[OPEN]

doi: 10.1105/tpc.17.00514

Figure Lengend Snippet: An Illustration of Bionano Contigs Likely Spanning Centromeric Regions in the G. herbaceum Reference.

Article Snippet: Bionano contigs are illustrated as cyan bars with a light blue coverage plot and many dark blue vertical BssSI matches to the genome sequence.

Techniques:

Journal: The Plant Cell

Article Title: Is It Ordered Correctly? Validating Genome Assemblies by Optical Mapping ^[OPEN]

doi: 10.1105/tpc.17.00514

Figure Lengend Snippet: Sequence Contigs from G. herbaceum Chromosome 4 Ordered and Oriented into Pseudomolecules by the Hi-C Methodology (as Assembled by PhaseGenomics).

Article Snippet: Bionano contigs are illustrated as cyan bars with a light blue coverage plot and many dark blue vertical BssSI matches to the genome sequence.

Techniques: Sequencing, Hi-C

Journal: bioRxiv

Article Title: Improvement of the threespine stickleback ( Gasterosteus aculeatus ) genome using a Hi-C-based Proximity-Guided Assembly method

doi: 10.1101/068528

Figure Lengend Snippet: PGA clusters all linkage groups of the G. aculeatus genome. The revised G. aculeatus genome assembly was divided into contiguous 50 kb contigs and assembled using proximity-guided assembly (PGA). The G. aculeatus revised reference assembly contig order is preserved along the X-axis. PGA clustering was largely congruent with the revised G. aculeatus reference genome, as shown by each linkage group (LG) assembled as a contiguous segment. Seven contigs were assigned to different linkage groups in the PGA clustering than in the reference assembly. For example, a contig that was assigned to LG IX in the reference assembly is assigned to LG III in the PGA cluster (brown dot in the lower left part of the figure).

Article Snippet: We split the G. aculeatus revised genome assembly ( ) into 4,377 consecutive 100 kb bins (the minimum recommended contig length for BioNano assemblies) for rescaffolding with the BioNano optical map contigs.

Techniques:

Journal: bioRxiv

Article Title: Improvement of the threespine stickleback ( Gasterosteus aculeatus ) genome using a Hi-C-based Proximity-Guided Assembly method

doi: 10.1101/068528

Figure Lengend Snippet: PGA clusters a large proportion of previously unassembled contigs to linkage groups. The revised G. aculeatus genome assembly was split into contigs at gaps and clustered with proximity-guided assembly (PGA) along with 21.7 Mb of contigs previously unassigned to linkage groups in the G. aculeatus genome. The G. aculeatus revised reference assembly contig order is preserved along the X-axis. The previously unassembled contigs (green vertical band) are distributed across linkage groups (LG) by the PGA clustering. PGA is less accurate clustering the G. aculeatus genome when the unassembled contigs are included, shown by an increased number of contigs being incorrectly assigned to different linkage groups (127 incorrectly assigned contigs, 0.94% of the previously assembled contig count).

Article Snippet: We split the G. aculeatus revised genome assembly ( ) into 4,377 consecutive 100 kb bins (the minimum recommended contig length for BioNano assemblies) for rescaffolding with the BioNano optical map contigs.

Techniques: