HiCLift: a fast and efficient tool for converting chromatin interaction data between genome assemblies.
HiCLift: a fast and efficient tool for converting chromatin interaction data between genome assemblies.
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DOI：
10.1093/bioinformatics/btad389
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发表时间：
2023-06-01
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随着人类参考基因组质量的不断提高和个体基因组数量的不断增加，基因组序列间的坐标转换在许多整合和比较研究中变得至关重要。虽然已经开发了用于线性基因组信号（如ChIP-Seq）的工具，但尽管三维基因组组织在基因调控和疾病中很重要，但还没有工具可以将基因组组装转化为染色质相互作用数据。在这里，我们介绍了HiCLift，一种快速有效的工具，可以将染色质接触（如Hi-C和Micro-C）的基因组坐标从一个组装转换到另一个组装，包括最新的T2T-CHM13基因组。与直接将原始reads重新映射到不同基因组的策略相比，HiCLift的运行速度平均快42倍（小时vs.天），同时输出几乎相同的接触矩阵。更重要的是，由于HiCLift不需要重新绘制原始读数，它可以直接转换人类患者样本数据，而原始测序读数有时很难获得或不可用。HiCLift可在https://github.com/XiaoTaoWang/HiCLift公开获取。
With the continuous effort to improve the quality of human reference genome and the generation of more and more personal genomes, the conversion of genomic coordinates between genome assemblies is critical in many integrative and comparative studies. While tools have been developed for such task for linear genome signals such as ChIP-Seq, no tool exists to convert genome assemblies for chromatin interaction data, despite the importance of three-dimensional genome organization in gene regulation and disease. Here, we present HiCLift, a fast and efficient tool that can convert the genomic coordinates of chromatin contacts such as Hi-C and Micro-C from one assembly to another, including the latest T2T-CHM13 genome. Comparing with the strategy of directly remapping raw reads to a different genome, HiCLift runs on average 42 times faster (hours vs. days), while outputs nearly identical contact matrices. More importantly, as HiCLift does not need to remap the raw reads, it can directly convert human patient sample data, where the raw sequencing reads are sometimes hard to acquire or not available. HiCLift is publicly available at https://github.com/XiaoTaoWang/HiCLift.
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影响因子：
56.9
作者：
Nurk, Sergey;Koren, Sergey;Rhie, Arang;Rautiainen, Mikko;Bzikadze, Andrey V;Mikheenko, Alla;Vollger, Mitchell R;Altemose, Nicolas;Uralsky, Lev;Gershman, Ariel;Aganezov, Sergey;Hoyt, Savannah J;Diekhans, Mark;Logsdon, Glennis A;Alonge, Michael;Antonarakis, Stylianos E;Borchers, Matthew;Bouffard, Gerard G;Brooks, Shelise Y;Caldas, Gina V;Chen, Nae-Chyun;Cheng, Haoyu;Chin, Chen-Shan;Chow, William;de Lima, Leonardo G;Dishuck, Philip C;Durbin, Richard;Dvorkina, Tatiana;Fiddes, Ian T;Formenti, Giulio;Fulton, Robert S;Fungtammasan, Arkarachai;Garrison, Erik;Grady, Patrick G S;Graves-Lindsay, Tina A;Hall, Ira M;Hansen, Nancy F;Hartley, Gabrielle A;Haukness, Marina;Howe, Kerstin;Hunkapiller, Michael W;Jain, Chirag;Jain, Miten;Jarvis, Erich D;Kerpedjiev, Peter;Kirsche, Melanie;Kolmogorov, Mikhail;Korlach, Jonas;Kremitzki, Milinn;Li, Heng;Maduro, Valerie V;Marschall, Tobias;McCartney, Ann M;McDaniel, Jennifer;Miller, Danny E;Mullikin, James C;Myers, Eugene W;Olson, Nathan D;Paten, Benedict;Peluso, Paul;Pevzner, Pavel A;Porubsky, David;Potapova, Tamara;Rogaev, Evgeny I;Rosenfeld, Jeffrey A;Salzberg, Steven L;Schneider, Valerie A;Sedlazeck, Fritz J;Shafin, Kishwar;Shew, Colin J;Shumate, Alaina;Sims, Ying;Smit, Arian F A;Soto, Daniela C;Sovic, Ivan;Storer, Jessica M;Streets, Aaron;Sullivan, Beth A;Thibaud-Nissen, Francoise;Torrance, James;Wagner, Justin;Walenz, Brian P;Wenger, Aaron;Wood, Jonathan M D;Xiao, Chunlin;Yan, Stephanie M;Young, Alice C;Zarate, Samantha;Surti, Urvashi;McCoy, Rajiv C;Dennis, Megan Y;Alexandrov, Ivan A;Gerton, Jennifer L;O'Neill, Rachel J;Timp, Winston;Zook, Justin M;Schatz, Michael C;Eichler, Evan E;Miga, Karen H;Phillippy, Adam M
通讯作者：
Phillippy, Adam M
影响因子：
64.5
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Quinodoz SA;Ollikainen N;Tabak B;Palla A;Schmidt JM;Detmar E;Lai MM;Shishkin AA;Bhat P;Takei Y;Trinh V;Aznauryan E;Russell P;Cheng C;Jovanovic M;Chow A;Cai L;McDonel P;Garber M;Guttman M
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Guttman M
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影响因子：
30.8
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Battaglia, Sofia;Dong, Kevin;Wu, Jingyi;Chen, Zeyu;Najm, Fadi J.;Zhang, Yuanyuan;Moore, Molly M.;Hecht, Vivian;Shoresh, Noam;Bernstein, Bradley E.
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Bernstein, Bradley E.
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