LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data.
LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data.
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Loretta，一种用户友好的工具，用于从PACBIO序列数据组装病毒基因组。
DOI：
10.1093/ve/veab042
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发表时间：
2021-01
期刊：
影响因子：
5.3
通讯作者：
Camiolo S
中科院分区：
文献类型：
--
作者：
Al Qaffas A;Nichols J;Davison AJ;Ourahmane A;Hertel L;McVoy MA;Camiolo S
Long-read, single-molecule DNA sequencing technologies have triggered a revolution in genomics by enabling the determination of large, reference-quality genomes in ways that overcome some of the limitations of short-read sequencing. However, the greater length and higher error rate of the reads generated on long-read platforms make the tools used for assembling short reads unsuitable for use in data assembly and motivate the development of new approaches. We present LoReTTA (Long Read Template-Targeted Assembler), a tool designed for performing de novo assembly of long reads generated from viral genomes on the PacBio platform. LoReTTA exploits a reference genome to guide the assembly process, an approach that has been successful with short reads. The tool was designed to deal with reads originating from viral genomes, which feature high genetic variability, possible multiple isoforms, and the dominant presence of additional organisms in clinical or environmental samples. LoReTTA was tested on a range of simulated and experimental datasets and outperformed established long-read assemblers in terms of assembly contiguity and accuracy. The software runs under the Linux operating system, is designed for easy adaptation to alternative systems, and features an automatic installation pipeline that takes care of the required dependencies. A command-line version and a user-friendly graphical interface version are available under a GPLv3 license at https://bioinformatics.cvr.ac.uk/software/ with the manual and a test dataset.
释放难以序列的噬菌体基因组的奥秘：Pap1甲基体和细菌免疫。
影响因子：
4.4
作者：
Lu S;Le S;Tan Y;Li M;Liu C;Zhang K;Huang J;Chen H;Rao X;Zhu J;Zou L;Ni Q;Li S;Wang J;Jin X;Hu Q;Yao X;Zhao X;Zhang L;Huang G;Hu F
通讯作者：
Hu F