Assemble zip code paper easily

Aug 6th, 2022
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How to assemble zip code paper

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BUSCO (Benchmarking Universal Single-Copy Orthologs) provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs.
BUSCO actually stands for Benchmarking Universal Single-Copy Orthologs and labels itself as a quality measure of the assembly.
Completeness is often measured using BUSCO (Benchmarking Universal Single-Copy Orthologs) scores, which look for the presence or absence of highly conserved genes in an assembly. The aim is to have the highest percentage of genes identified in your assembly, with a BUSCO complete score above 95% considered good.
BUSCO (Benchmarking Universal Single-Copy Orthologs) provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs.
BUSCO actually stands for Benchmarking Universal Single-Copy Orthologs and labels itself as a quality measure of the assembly.
BUSCO is a tool to assess completeness of genome assembly, gene set and transcriptome. It is based on the concept of single-copy orthologs that should be highly conserved among the closely related species.
Completeness is often measured using BUSCO (Benchmarking Universal Single-Copy Orthologs) scores, which look for the presence or absence of highly conserved genes in an assembly. The aim is to have the highest percentage of genes identified in your assembly, with a BUSCO complete score above 95% considered good.
Interpreting the results. BUSCO attempts to provide a quantitative assessment of the completeness in terms of expected gene content of a genome assembly, transcriptome, or annotated gene set. The results are simplified into categories of Complete and single-copy, Complete and duplicated, Fragmented, or Missing BUSCOs.
Roughly, completeness is the number of unique SCGs present within the bin / the number of unique SCGs in the list. Contamination is estimated by looking at how many SCGs are present in multiple copies, as only one copy should be present of each SCG per genome.
Subsequent filtering, e.g. on sequence uniqueness and conservation levels [see Supplementary Online Material (SOM) for details], resulted in BUSCO sets representing 3023 genes for vertebrates, 2675 for arthropods, 843 for metazoans, 1438 for fungi and 429 for eukaryotes.

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