Max Planck Institute for Developmental Biology, Tübingen 72076, Germany.
Bioinformatics. 2021 Nov 5;37(21):3929-3931. doi: 10.1093/bioinformatics/btab613.
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.
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 data are available at Bioinformatics online.
纤毛虫是单细胞真核生物，在发育过程中会从基因组中消除特定的、分散的 DNA 序列（内部消除序列，IESs）。这些序列难以注释和组装，因为含有 IES 的序列在细胞中的丰度通常比不含 IES 的序列低得多，而 IES 序列本身通常含有重复和低复杂度的序列。Pacific Biosciences 和 Oxford Nanopore 的长读测序技术有可能比短读测序重建更长的 IES，但需要不同的组装策略。本文介绍了 BleTIES，这是一个使用映射长读检测、组装和分析 IES 的软件工具包。
BleTIES 是用 Python 3 实现的。源代码可在 https://github.com/Swart-lab/bleties（MIT 许可证）获得，也可通过 Bioconda 分发。
补充数据可在 Bioinformatics 在线获得。
