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. 2020 Dec 21;70(12):2337–2348. doi: 10.1136/gutjnl-2020-323300

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© Author(s) (or their employer(s)) 2021. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.

This is an open access article distributed in accordance with the Creative Commons Attribution Non Commercial (CC BY-NC 4.0) license, which permits others to distribute, remix, adapt, build upon this work non-commercially, and license their derivative works on different terms, provided the original work is properly cited, appropriate credit is given, any changes made indicated, and the use is non-commercial. See: http://creativecommons.org/licenses/by-nc/4.0/.

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Bioinformatic workflow for the identification of chimeric HBV human sequences. Following quality control (by Trimmomatic), sequencing reads were aligned to virus-specific genome by Burrows Wheeler Aligner-Maximal Exaxt Matches (BWA-MEM) in order to extract all reads that contained HBV fragments. SAMtools software was applied to extrapolate all chimeric HBV human sequences, representing the HBV integrations into human genome. ANNOVAR software was used to map HBV integrations at chromosome and gene level. The functionality of genes involved in HBV integration was retrieved by Gene Cards, Protein Atlas and KEGG databases. WES, whole exome sequencing.