Summary Ciliates are single-celled eukaryotes that eliminate specific, interspersed DNA sequences (internally eliminated sequences, IESs) from their genomes during development. These are challenging to annotate and assemble because IES-containing sequences are typically much less abundant in the cell than those without, and IES sequences themselves often contain repetitive and low-complexity sequences. Long-read sequencing technologies from Pacific Biosciences and Oxford Nanopore have the potential to reconstruct longer IESs than has been possible with short reads but require a different assembly strategy. Here we present BleTIES, a software toolkit for detecting, assembling, and analyzing IESs using mapped long reads. Availability and implementation BleTIES is implemented in Python 3. Source code is available at https://github.com/Swart-lab/bleties (MIT license) and also distributed via Bioconda. Supplementary information Supplementary data are available at Bioinformatics online.

中文翻译：

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BleTIES：使用长读长测序注释纤毛虫自然基因组编辑


摘要 纤毛虫是单细胞真核生物，在发育过程中从其基因组中消除特定的、散布的 DNA 序列（内部消除序列，IES）。这些注释和组装具有挑战性，因为含有 IES 的序列在细胞中通常比不含 IES 的序列丰富得多，而且 IES 序列本身通常包含重复和低复杂性序列。 Pacific Biosciences 和 Oxford Nanopore 的长读长测序技术有可能重建比短读长更长的 IES，但需要不同的组装策略。在这里，我们介绍 BleTIES，一个使用映射长读长检测、组装和分析 IES 的软件工具包。可用性和实现 BleTIES 在 Python 3 中实现。源代码可在 https://github.com/Swart-lab/bleties（MIT 许可证）获取，也可通过 Bioconda 分发。补充信息 补充数据可在生物信息学在线获取。