Journal: Scientific Data

Article Title: A European-wide dataset to uncover adaptive traits of Listeria monocytogenes to diverse ecological niches

doi: 10.1038/s41597-022-01278-6

Figure Lengend Snippet: Microreact screenshot representing the distribution of the whole LISTADAPT dataset (n = 1484) by geographic region ( a ) and time ( b ). The k-mer-based phylogenomic clustering of the complete dataset is shown in ( c ). Interactive access to strain metadata and MLST types is available through Microreact , a recently developed online tool for visualizing and sharing spacio-temporal and genetic distributions of strains (Fig. 2, accession link: https://microreact.org/project/8YtGBqEqhosJtysXTVY79M-figure-2-distribution-of-the-whole-listadapt-dataset-n1484-by-geographic-region-time-and-genetic-diversity ). The dataset interactive map was generated using either the exact GPS coordinate, regional GPS coordinate or national GPS coordinate according to the level of details available for each strain. An annual timescale was used. The core genome MLST (Moura et al .) tree was generated from the draft genome assemblies using pairwise categorical difference and single linkage method in BioNumerics. The tree revealed three main clades corresponding to Lm phylogenetic lineages. Each clade included several clusters corresponding to MLST types (CC and singleton ST). Circles in shade of blue show food product isolates (clear blue: fish product, greeblue: dairy products, blue: composite dishes, deep blue: meat products). Circles in shade of orange show animal and environment isolates (beige: soil & farm environment, golden: wild animal, deep orange: farm animals). Circles size is proportional to the number of strains included.

Article Snippet: Reads normalized to 100 × coverage, draft assemblies (contigs and scaffolds) and annotated genomes (Genome Feature Format, GFF, and Genbank format, GBK) were also centralized at the MongoDB database located at ANSES (Maisons-Alfort Laboratory for Food Safety) providing quickly available, ready-to-use data.

Techniques: Generated

Journal: BMC Genomics

Article Title: RAD tag sequencing as a source of SNP markers in Cynara cardunculus L

doi: 10.1186/1471-2164-13-3

Figure Lengend Snippet: Contig length distribution and the efficiency of SNP discovery . Red bars represent the portion of contigs having no SNP identified, while green bars represent contigs harbouring at least one SNP.

Article Snippet: A RAD LongRead ® contig assembly was generated by a set of algorithms developed at Floragenex Inc. Sequences having more than 5 bases with poor Illumina quality scores (Phred10 or lower) were discarded.

Techniques:

Journal: BMC Genomics

Article Title: RAD tag sequencing as a source of SNP markers in Cynara cardunculus L

doi: 10.1186/1471-2164-13-3

Figure Lengend Snippet: Comparison of K-mer spectra in the C. cardunculus RAD contig assembly vs the full genomes of A. thaliana , V. vinifera and F. vesca . K-mer (k = 10) distribution for C. cardunculus (A) was evaluated both on pre-assembly sequence data (outer box) and contig sequences (inner box). K-mer populations have been split on the basis of their CpG content. × axis represents the number of occurrences of a given 10-mer; Y axis reports the amount of different 10-mers reporting that occurrence count.

Article Snippet: A RAD LongRead ® contig assembly was generated by a set of algorithms developed at Floragenex Inc. Sequences having more than 5 bases with poor Illumina quality scores (Phred10 or lower) were discarded.

Techniques: Comparison, Sequencing

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: bioRxiv

Article Title: SLR-superscaffolder: a de novo scaffolding tool for synthetic long reads using a top-to-bottom scheme

doi: 10.1101/762385

Figure Lengend Snippet: Scaffolding model of the correlation between two contigs, ordering of three contigs and orientating of a given contig by its neighboring contig with using co-barcoding information.

Article Snippet: In this work, three draft assemblies of HG001 were used as input, including the contigs assembled by MaSuRCA [ ] with stLFR reads only (MaSuRCA contigs), the scaffolds assembled by SOAP denovo2 [ ] with stLFR reads and an additional 20-fold PE PCR-free NGS dataset (SOAP denovo scaffolds) and the contigs assembled by Canu[ ] with about 30-fold Oxford Nanopore technology (ONT) reads from (ONT contigs) Jain et al. work[ ].

Techniques: Scaffolding

Journal: bioRxiv

Article Title: SLR-superscaffolder: a de novo scaffolding tool for synthetic long reads using a top-to-bottom scheme

doi: 10.1101/762385

Figure Lengend Snippet: Quality of scaffolds assembled by SLR-superscaffolder with different length thresholds of seed contigs.

Article Snippet: In this work, three draft assemblies of HG001 were used as input, including the contigs assembled by MaSuRCA [ ] with stLFR reads only (MaSuRCA contigs), the scaffolds assembled by SOAP denovo2 [ ] with stLFR reads and an additional 20-fold PE PCR-free NGS dataset (SOAP denovo scaffolds) and the contigs assembled by Canu[ ] with about 30-fold Oxford Nanopore technology (ONT) reads from (ONT contigs) Jain et al. work[ ].

Techniques:

Journal: bioRxiv

Article Title: SLR-superscaffolder: a de novo scaffolding tool for synthetic long reads using a top-to-bottom scheme

doi: 10.1101/762385

Figure Lengend Snippet: Histograms of time consumption of four scaffolders (SLR-superscaffolder, fragScaff, Architect, ARKS) for three input assemblies (MaSuRCA contigs, SOAP denovo scaffolds, Canu contigs).

Article Snippet: In this work, three draft assemblies of HG001 were used as input, including the contigs assembled by MaSuRCA [ ] with stLFR reads only (MaSuRCA contigs), the scaffolds assembled by SOAP denovo2 [ ] with stLFR reads and an additional 20-fold PE PCR-free NGS dataset (SOAP denovo scaffolds) and the contigs assembled by Canu[ ] with about 30-fold Oxford Nanopore technology (ONT) reads from (ONT contigs) Jain et al. work[ ].

Techniques:

Journal: GigaScience

Article Title: A critical comparison of technologies for a plant genome sequencing project

doi: 10.1093/gigascience/giy163

Figure Lengend Snippet: Comparison of contig/scaffold lengths and total assembly sizes of the various S. verrucosum assemblies.

Article Snippet: For example, the discovar-mp-dt-bn assembly is the discovar contig assembly scaffolded first with mate-pairs, then Dovetail and finally BioNano.

Techniques: Comparison

Journal: GigaScience

Article Title: A critical comparison of technologies for a plant genome sequencing project

doi: 10.1093/gigascience/giy163

Figure Lengend Snippet: Assembly statistics of Illumina and PacBio assemblies, with a minimum contig/scaffold size of 1 kbp

Article Snippet: For example, the discovar-mp-dt-bn assembly is the discovar contig assembly scaffolded first with mate-pairs, then Dovetail and finally BioNano.

Techniques:

Journal: GigaScience

Article Title: A critical comparison of technologies for a plant genome sequencing project

doi: 10.1093/gigascience/giy163

Figure Lengend Snippet: k -mer spectra plots from the k -mer Analysis Toolkit comparing three S. verrucosum contig assemblies. The heights of the bars indicate how many k -mers of each multiplicity appear in the raw Discovar reads. The colors indicate how many times those k -mers appear in the respective assemblies with black being zero times and red being one time. A colored bar at zero multiplicity indicates k -mers appearing in the assembly that do not appear in the reads. The Falcon assembly has been polished with the Illumina reads using Pilon to reduce the effect of using a different sequencing platform.

Article Snippet: For example, the discovar-mp-dt-bn assembly is the discovar contig assembly scaffolded first with mate-pairs, then Dovetail and finally BioNano.

Techniques: Sequencing

Journal: GigaScience

Article Title: A critical comparison of technologies for a plant genome sequencing project

doi: 10.1093/gigascience/giy163

Figure Lengend Snippet: Busco analysis of supernova-bn , discovar-mp-dt-bn , and falcon-dt-bn using the plant gene dataset.

Article Snippet: For example, the discovar-mp-dt-bn assembly is the discovar contig assembly scaffolded first with mate-pairs, then Dovetail and finally BioNano.

Techniques:

Journal: GigaScience

Article Title: A critical comparison of technologies for a plant genome sequencing project

doi: 10.1093/gigascience/giy163

Figure Lengend Snippet: Box and whisker plot showing completeness of the S. tuberosum transcripts in supernova-bn , discovar-mp-dt-bn , and falcon-dt-bn with various levels of minimum percentage identity.

Article Snippet: For example, the discovar-mp-dt-bn assembly is the discovar contig assembly scaffolded first with mate-pairs, then Dovetail and finally BioNano.

Techniques: Whisker Assay

Journal: GigaScience

Article Title: A critical comparison of technologies for a plant genome sequencing project

doi: 10.1093/gigascience/giy163

Figure Lengend Snippet: A difficult region of the genome that is contiguously assembled with a PacBio BAC but in none of our whole-genome assemblies. The region was correctly scaffolded by Dovetail. The figure shows various alignments and information with respect to the BAC assembly. The top track shows the contigs that appear in the discovar , falcon , and supernova assemblies. The paired-end track shows read coverage of the Discovar paired-end library. The mate-pair and Dovetail tracks show physical/fragment coverage of the mate-pair and Dovetail libraries, respectively. The bottom track shows GC content of the sequence as well as homopolymers sequences of at least 5 bp where A, C, G, and T are colored red, blue, yellow, and green, respectively.

Article Snippet: For example, the discovar-mp-dt-bn assembly is the discovar contig assembly scaffolded first with mate-pairs, then Dovetail and finally BioNano.

Techniques: Sequencing

Journal: GigaScience

Article Title: A critical comparison of technologies for a plant genome sequencing project

doi: 10.1093/gigascience/giy163

Figure Lengend Snippet: Material requirements for each library

Article Snippet: For example, the discovar-mp-dt-bn assembly is the discovar contig assembly scaffolded first with mate-pairs, then Dovetail and finally BioNano.

Techniques:

Journal: GigaScience

Article Title: A critical comparison of technologies for a plant genome sequencing project

doi: 10.1093/gigascience/giy163

Figure Lengend Snippet: The overall cost of each assembly project

Article Snippet: For example, the discovar-mp-dt-bn assembly is the discovar contig assembly scaffolded first with mate-pairs, then Dovetail and finally BioNano.

Techniques:

Journal: GigaScience

Article Title: A critical comparison of technologies for a plant genome sequencing project

doi: 10.1093/gigascience/giy163

Figure Lengend Snippet: Computational requirements

Article Snippet: For example, the discovar-mp-dt-bn assembly is the discovar contig assembly scaffolded first with mate-pairs, then Dovetail and finally BioNano.

Techniques: