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: PLoS ONE

Article Title: Evaluating the Fidelity of De Novo Short Read Metagenomic Assembly Using Simulated Data

doi: 10.1371/journal.pone.0019984

Figure Lengend Snippet: Summary of the assembly statistics of the simulated datasets.

Article Snippet: For instance, the 400 bp HC dataset produced 11.0 and 17.4 Mb of correctly annotated contigs assembled with Newbler and Celera respectively, while the 110 bp HChc dataset produced 171 Mbs and 275 Mbs (with SSAKE and VELVET respectively).

Techniques:

Journal: PLoS ONE

Article Title: Evaluating the Fidelity of De Novo Short Read Metagenomic Assembly Using Simulated Data

doi: 10.1371/journal.pone.0019984

Figure Lengend Snippet: (A) 400 bp and (B) 110 bp datasets respectively. N stands for Newbler, C for Celera Assembler, S for SSAKE and V for Velvet.

Article Snippet: For instance, the 400 bp HC dataset produced 11.0 and 17.4 Mb of correctly annotated contigs assembled with Newbler and Celera respectively, while the 110 bp HChc dataset produced 171 Mbs and 275 Mbs (with SSAKE and VELVET respectively).

Techniques:

Journal: PLoS ONE

Article Title: Evaluating the Fidelity of De Novo Short Read Metagenomic Assembly Using Simulated Data

doi: 10.1371/journal.pone.0019984

Figure Lengend Snippet: (A) Newbler (400 bp datasets) and (B) Velvet (110 bp datasets) assemblies.

Article Snippet: For instance, the 400 bp HC dataset produced 11.0 and 17.4 Mb of correctly annotated contigs assembled with Newbler and Celera respectively, while the 110 bp HChc dataset produced 171 Mbs and 275 Mbs (with SSAKE and VELVET respectively).

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:

Article Title: AglZ Is a Filament-Forming Coiled-Coil Protein Required for Adventurous Gliding Motility of Myxococcus xanthus

doi: 10.1128/JB.186.18.6168-6178.2004

Figure Lengend Snippet: Cloning of the aglZ gene. A 784-bp partial sequence of aglZ was recovered from the yeast two-hybrid library and named pAGS152. The 5′ end of the aglZ gene and upstream DNA sequence were recovered by matching with contig MYX10C862 from the Monsanto Microbial Genome database of the M. xanthus genome. The 3′ end of the aglZ gene and the downstream gene were recovered by integration of a partial aglZ clone, pAGS164, into the M. xanthus chromosome. Chromosomal DNA was digested with SacI to yield pAGS160. The 2-kb fragment subcloned from pAGS160 was used as a probe to identify a 6-kb fragment containing aglZ from the λ-ZAP library.

Article Snippet: Contigs MYX10C862 and MYX10C1267 from the Cereon Microbial Genome database (Monsanto) each aligned with a part of the sequence.

Techniques: Cloning, Sequencing