![]() Run_busco_after_hi-C/full_table_busco_after_hi-C.tsv:EOG090C00C9 Missing We therefore analyzed the steps performed by BUSCO to search for BUSCO-matching genes in the genome and noted that theģ1 genomic regions supporting BUSCOs before scaffolding were not reported in the tBLASTn results filesĬoordinates_busco_after_hi-C.tsv or coordinates_busco_after_hi-C_missing_and_frag_rerun.tsv ofĪlignments performed on the assembly after scaffolding.Įxample with EOG090C00C9 Final results for EOG090C00C9 This means that theģ1 genomic regions supporting the BUSCOs before scaffolding are integrally conserved in the assembly after scaffolding. Scaffolding (according to the full table tsv file) were concerned by the 3D-DNA misjoin correction step. After analysis, it appears that none of the 31 genomic regions supporting the BUSCOs before Indeed, theģD-DNA pipeline used to scaffold the contigs performs a misjoin detection and correction step which could lead to contigįragmentation. Why are some BUSCO genes no longer found in the assembly after scaffolding? To answer this question, we suspected that someĬontigs may have been fragmented during the scaffolding process. BUSCO genes found before and missing after scaffolding ![]() 15 BUSCO genes are missing before scaffolding and foundĪfter and more surprisingly 31 BUSCO genes are found before scaffolding and missing after. Missing BUSCO genes and the 71 missing after scaffolding, only 40 were common. We focused our attention on the missing BUSCO gene lists and we observed that among the 55 before scaffolding Results obtained before and after scaffolding are of course very close but the metrics degradation (except the fragmentedīUSCOs) puzzled us. Resulting BUSCO metrics Before Hi-C scaffolding After Hi-C scaffoldingĬ:97.8%,F:1.0%,M:1.2%,n:4584 C:97.6%,F:0.9%,M:1.5%,n:4584Ĥ482 Complete BUSCOs (C) 4472 Complete BUSCOs (C)Ĥ371 Complete and single-copy BUSCOs (S) 4363 Complete and single-copy BUSCOs (S)ġ11 Complete and duplicated BUSCOs (D) 109 Complete and duplicated BUSCOs (D)Ĥ7 Fragmented BUSCOs (F) 41 Fragmented BUSCOs (F)ĥ5 Missing BUSCOs (M) 71 Missing BUSCOs (M)Ĥ584 Total BUSCO groups searched 4584 Total BUSCO groups searched Python $BUSCO-DIRECTORY/scripts/run_BUSCO.py -i Perca_flavescens_scaffolds.fa -o busco_after_hi-C -l $BUSCO-DIRECTORY/datasets/actinopterygii_odb9 -m genome -c 6 -limit 10 -sp zebrafish Python $BUSCO-DIRECTORY/scripts/run_BUSCO.py -i Perca_flavescens_contigs.fa -o busco_before_hiC -l $BUSCO-DIRECTORY/datasets/actinopterygii_odb9 -m genome -c 6 -limit 10 -sp zebrafish BUSCO v3.0.2 was run on both genome assembly versions using the following command lines.
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