BAMscale: quantification of DNA sequencing peaks and generation of scaled coverage tracks

Pongor, L. S.; Gross, J. M.; Vera Alvarez, R.; Murai, J.; Jang, S.-M.; Zhang, H.; Redon, C.; Fu, H.; Huang, S.-Y.; Thakur, B.; Baris, A.; Marino-Ramirez, L.; Landsman, D.; Mirit, A. I.; Pommier, Y.

doi:10.1101/669275

bioRxiv · 10.1101/669275

BAMscale: quantification of DNA sequencing peaks and generation of scaled coverage tracks

Pongor, L. S.·Gross, J. M.·Vera Alvarez, R.·Murai, J.·Jang, S.-M.·Zhang, H.·Redon, C.·Fu, H.·Huang, S.-Y.·Thakur, B.·Baris, A.·Marino-Ramirez, L.·Landsman, D.·Mirit, A. I.·Pommier, Y.

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Abstract

BAMscale is a one-step tool that processes DNA sequencing datasets from chromatin binding (ChIP-seq) and chromatin state changes (ATAC-seq, END-seq) experiments to DNA replication data (OK-seq, NS-seq and replication timing). The outputs include normalized peak scores in text format and scaled coverage tracks (BigWig) which are directly accessible to data visualization programs. BAMscale (available at https://github.com/ncbi/BAMscale) effectively processes large sequencing datasets (~100Gb size) in minutes, outperforming currently available tools.

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Pongor, L. S., Gross, J. M., Vera Alvarez, R., Murai, J., Jang, S.-M., Zhang, H., Redon, C., Fu, H., Huang, S.-Y., Thakur, B., Baris, A., Marino-Ramirez, L., Landsman, D., Mirit, A. I., Pommier, Y.. 2019-06-13. BAMscale: quantification of DNA sequencing peaks and generation of scaled coverage tracks. https://doi.org/10.1101/669275

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