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: GigaScience

Article Title: SMRT long reads and Direct Label and Stain optical maps allow the generation of a high-quality genome assembly for the European barn swallow ( Hirundo rustica rustica )

doi: 10.1093/gigascience/giy142

Figure Lengend Snippet: Assembly metrics for contigs and final scaffolds in our European barn swallow genome

Article Snippet: Of 3,872 SMRT contigs, 1,243 (32%) were anchored in the Bionano maps, of which 990 were anchored in both NLRS and DLS maps, while 226 and 56 were anchored in NLRS and DLS maps, respectively; 2810 maps could not be anchored at all.

Techniques: