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: Evaluation of de novo transcriptome assemblies from RNA-Seq data

doi: 10.1101/006338

Figure Lengend Snippet: The DETONATE package workflow. The DETONATE package consists of two components: RSEM-EVAL and REF-EVAL. Combined, these two components allow for the computation of a variety of evaluation scores for a de novo transcriptome assembly. RSEM-EVAL produces an evaluation score that is based only on an assembly and the set of reads from which it was constructed. When a reference transcript set is available, REF-EVAL may be used to compute a number of reference-based measures. For most measures, REF-EVAL requires only an assembly and a reference transcript set. For weighted measures and measures with respect to an estimated “true” contig set, REF-EVAL additionally requires the set of reads that were assembled (dashed arrow).

Article Snippet: Lastly, RSEMEVAL currently only focuses on contig assemblies constructed from single-end Illumina RNA-Seq data.

Techniques: Construct

Journal: bioRxiv

Article Title: Evaluation of de novo transcriptome assemblies from RNA-Seq data

doi: 10.1101/006338

Figure Lengend Snippet: The different granularities of reference-based measures computed by REF-EVAL. (A) The contig level measure requires at least 99% alignment between a matched contig and reference sequence in a one-to-one mapping between an assembly and the reference. (B) The nucleotide level measure counts the number of correctly recovered nucleotides without requiring a one-to-one mapping. Unlike the contig level measure, it gives full credit to the two short contigs. The table on the right gives both the contig-level and nucleotide-level recall values for (A) and (B).

Article Snippet: Lastly, RSEMEVAL currently only focuses on contig assemblies constructed from single-end Illumina RNA-Seq data.

Techniques: Sequencing

Journal: bioRxiv

Article Title: Evaluation of de novo transcriptome assemblies from RNA-Seq data

doi: 10.1101/006338

Figure Lengend Snippet: Correlation of the RSEM-EVAL score with reference-based measures on the strand non-specific data sets. Scatterplots are shown for the simulated (top row) and real mouse (bottom row) data sets and for both the nucleotide-level F 1 (left column) and contig-level F 1 (center column) measures. For comparison, scatterplots of the nucleotide-level F 1 against the contig-level F 1 are shown (right column). The Spearman rank correlation coefficient (bottom-right corner of each plot) was computed for each combination of data set and reference-based measure.

Article Snippet: Lastly, RSEMEVAL currently only focuses on contig assemblies constructed from single-end Illumina RNA-Seq data.

Techniques: Comparison

Journal: bioRxiv

Article Title: Evaluation of de novo transcriptome assemblies from RNA-Seq data

doi: 10.1101/006338

Figure Lengend Snippet: RSEM-EVAL scores and Xenopus protein recovery for the axolotl blastema transcriptome assemblies. The y-axis represents the percent of proteins with at least x percent of their length (x-axis) recovered by an axolotl contig. The curve for each assembly is colored according to its RSEM-EVAL score, with red representing the highest RSEM-EVAL score. The assembly with the curve closest to the upper-right corner is the best in terms of its comparison with the Xenopus protein set.

Article Snippet: Lastly, RSEMEVAL currently only focuses on contig assemblies constructed from single-end Illumina RNA-Seq data.

Techniques: Comparison