MUM&Co: accurate detection of all SV types through whole-genome alignment
Abstract
MUM&Co is a single bash script to detect structural variations (SVs) utilizing whole-genome alignment (WGA). Using MUMmer’s nucmer alignment, MUM&Co can detect insertions, deletions, tandem duplications, inversions and translocations greater than 50 bp. Its versatility depends upon the WGA and therefore benefits from contiguous de-novo assemblies generated by third generation sequencing technologies. Benchmarked against five WGA SV-calling tools, MUM&Co outperforms all tools on simulated SVs in yeast, plant and human genomes and performs similarly in two real human datasets. Additionally, MUM&Co is particularly unique in its ability to find inversions in both simulated and real datasets. Lastly, MUM&Co’s primary output is an intuitive tabulated file containing a list of SVs with only necessary genomic details.
Domains
Life Sciences [q-bio]
Fichier principal
MUMandCo_unmarked.pdf (595.39 Ko)
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Supp_table1.xlsx (52.46 Ko)
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Supp_table2.xlsx (17.13 Ko)
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Supp_table3.xlsx (16.11 Ko)
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Supp_table4.xlsx (37.17 Ko)
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| Origin | Files produced by the author(s) |
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