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Formatted output figs
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GallVp committed Mar 1, 2024
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Expand Up @@ -59,7 +59,7 @@ The pipeline prints a warning in the pipeline log if FASTA or GFF3 validation fa

GenomeTools `gt stat` tool calculates a basic set of statistics about features contained in GFF3 files.

<div align="center"><figure><img src="images/FI1.gt.stat.yml.gene.length.png" alt="AssemblyQC - GenomeTools gt stat gene length distribution" width="50%"><figcaption>AssemblyQC - GenomeTools gt stat gene length distribution</figcaption><figure></div>
<div align="center"><img src="images/FI1.gt.stat.yml.gene.length.png" alt="AssemblyQC - GenomeTools gt stat gene length distribution" width="50%"><hr><em>AssemblyQC - GenomeTools gt stat gene length distribution</em></div>

### NCBI FCS adaptor

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[BUSCO estimates](https://busco.ezlab.org/busco_userguide.html) the completeness and redundancy of processed genomic data based on universal single-copy orthologs.

<div align="center"><figure><img src="images/busco_figure.png" alt="AssemblyQC - BUSCO summary plot" width="50%"><figcaption>AssemblyQC - BUSCO summary plot</figcaption><figure></div>
<div align="center"><img src="images/busco_figure.png" alt="AssemblyQC - BUSCO summary plot" width="50%"><hr><em>AssemblyQC - BUSCO summary plot</em></div>

### TIDK

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TIDK toolkit is designed to [identify and visualize](https://github.com/tolkit/telomeric-identifier) telomeric repeats for the Darwin Tree of Life genomes.

<div align="center"><figure><img src="images/tidk.png" alt="AssemblyQC - TIDK plot" width="50%"><figcaption>AssemblyQC - TIDK plot</figcaption><figure></div>
<div align="center"><img src="images/tidk.png" alt="AssemblyQC - TIDK plot" width="50%"><hr><em>AssemblyQC - TIDK plot</em></div>

### LAI

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Synteny plots are created with Circos which is a tool [facilitating](https://circos.ca) the identification and analysis of similarities and differences arising from comparisons of genomes. The genome-wide alignments are performed with [MUMMER](https://github.com/mummer4/mummer?tab=readme-ov-file) and bundled with [`dnadiff.pl`](https://github.com/mummer4/mummer/blob/master/scripts/dnadiff.pl).

<div align="center"><figure><img src="images/synteny.png" alt="AssemblyQC - Synteny plot" width="50%"><figcaption>AssemblyQC - Synteny plot</figcaption><figure></div>
<div align="center"><img src="images/synteny.png" alt="AssemblyQC - Synteny plot" width="50%"><hr><em>AssemblyQC - Synteny plot</em></div>

### Pipeline information

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