Software

LRSDAY (https://github.com/yjx1217/LRSDAY)

Long-read sequencing technologies have become increasingly popular in genome projects due to their strengths in resolving complex genomic regions. As a leading model organism with small genome size and great biotechnological importance, the budding yeast, Saccharomyces cerevisiae, has many isolates currently being sequenced with long reads. However, analyzing long-read sequencing data to produce high-quality genome assembly and annotation remains challenging. LRSDAY is the first one-stop solution to streamline this process. LRSDAY can produce chromosome-level end-to-end genome assembly and comprehensive annotations for various genomic features (including centromeres, protein-coding genes, tRNAs, transposable elements and telomere-associated elements) that are ready for downstream analysis. Although tailored for S. cerevisiae, we designed LRSDAY to be highly modular and customizable, making it adaptable for virtually any eukaryotic organisms.

simuG (https://github.com/yjx1217/simuG)

Simulated genomes with pre-defined and random genomic variants can be very useful for benchmarking genomic and bioinformatics analyses. Here we introduce simuG as a light-weighted tool for simulating the full spectrum of genomic variants (SNPs, INDELs, CNVs, inversions, and translocations). It also provides a rich array of options for fine-grained controls on the specific type and properties of variants to be introduced. The simplicity and versatility of simuG make it a unique general purpose genome simulator for a wide-range of simulation-based applications.

 

 

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