Earlham Institute, Norwich Research Park, Norwich, UK.
BMC Bioinformatics. 2021 Mar 16;22(1):124. doi: 10.1186/s12859-021-04056-0.
The analysis of long reads or the assessment of assembly or target capture data often necessitates running alignments against reference genomes or gene sets. The aligner outputs are often parsed automatically by scripts, but many kinds of analysis can benefit from the understanding that can follow human inspection of individual alignments. Additionally, diagrams are a useful means of communicating assembly results to others.
We developed Alvis, a simple command line tool that can generate visualisations for a number of common alignment analysis tasks. Alvis is a fast and portable tool that accepts input in a variety of alignment formats and will output production ready vector images. Additionally, Alvis will highlight potentially chimeric reads or contigs, a common source of misassemblies.
Alvis diagrams facilitate improved understanding of assembly quality, enable read coverage to be visualised and potential errors to be identified. Additionally, we found that splitting chimeric reads using the output provided by Alvis can improve the contiguity of assemblies, while maintaining correctness.
长读段的分析或组装或目标捕获数据的评估通常需要针对参考基因组或基因集运行比对。比对器输出通常由脚本自动解析，但许多类型的分析可以从人工检查单个比对中受益。此外，图表是向他人传达组装结果的有用手段。
我们开发了 Alvis，这是一个简单的命令行工具，可以为许多常见的对齐分析任务生成可视化效果。Alvis 是一个快速且可移植的工具，它接受各种对齐格式的输入，并将输出可用于生产的矢量图像。此外，Alvis 将突出显示潜在的嵌合体读取或重叠群，这是组装错误的常见来源。
Alvis 图有助于更好地理解组装质量，能够可视化读取覆盖度并识别潜在错误。此外，我们发现使用 Alvis 提供的输出拆分嵌合体读取可以提高组装的连续性，同时保持正确性。
