ACEseq - allele specific copy number estimation from whole genome sequencing

Kleinheinz, K.; Bludau, I.; Huebschmann, D.; Heinold, M.; Kensche, P.; Gu, Z.; Lopez, C.; Hummel, M.; Klapper, W.; Moeller, P.; Vater, I.; Wagener, R.; ICGC MMML-Seq project,; Brors, B.; Siebert, R.; Eils, R.; Schlesner, M.

doi:10.1101/210807

bioRxiv · 10.1101/210807

ACEseq - allele specific copy number estimation from whole genome sequencing

Kleinheinz, K.·Bludau, I.·Huebschmann, D.·Heinold, M.·Kensche, P.·Gu, Z.·Lopez, C.·Hummel, M.·Klapper, W.·Moeller, P.·Vater, I.·Wagener, R.·ICGC MMML-Seq project,·Brors, B.·Siebert, R.·Eils, R.·Schlesner, M.

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Abstract

ACEseq is a computational tool for allele-specific copy number estimation in tumor genomes based on whole genome sequencing. In contrast to other tools it features GC-bias correction, unique replication timing-bias correction and integration of structural variant (SV) breakpoints for improved genome segmentation. ACEseq clearly outperforms widely used state-of-the art methods, provides a fully automated estimation of tumor cell content and ploidy, and additionally computes homologous recombination deficiency scores.

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Kleinheinz, K., Bludau, I., Huebschmann, D., Heinold, M., Kensche, P., Gu, Z., Lopez, C., Hummel, M., Klapper, W., Moeller, P., Vater, I., Wagener, R., ICGC MMML-Seq project,, Brors, B., Siebert, R., Eils, R., Schlesner, M.. 2017-10-29. ACEseq - allele specific copy number estimation from whole genome sequencing. https://doi.org/10.1101/210807

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