Data for "A replicable and modular benchmark for long-read transcript quantification methods"

This dataset was used in the paper titled "A replicable and modular benchmark for long-read transcript quantification methods". It contains simulated ONT and PacBio datasets as follows:

Mouse PacBio and ONT Datasets:

The PacBio dataset is available at Zenodo record 11201284. It was simulated with an overall error rate of 1.4%, following the methodology described in Prjibelski et al., 2023.

The ONT dataset was derived from the R10.4 dataset available at Zenodo record 7121404. Reads were extracted by converting the BAM file to FASTQ format and then shuffled using the shuffle.sh utility from the BBMap suite. Simulation was performed using NanoSim with an error rate of 2.8%. The default NanoSim behavior of introducing background "unaligned" reads was disabled to ensure a cleaner simulation.

ONT cDNA and Direct RNA Datasets (NA12878 cell line):

These datasets were simulated using NanoSim based on the NA12878 sample from the Nanopore WGS Consortium.

ONT Direct RNA Dataset with Realistic Truncation (NA12878 cell line): 

This dataset was simulated using a combination of DRSim and Badread, based on the NA12878 sample. DRSim was used to model realistic 3′-end truncation patterns, while Badread simulated the Nanopore sequencing error profile. Further details are provided in the paper referenced above.

This archive contains all input files necessary to run the initial benchmarks associated with the lr_quant_benchmarks repository.

The archive can be decompressed with tar and zstd using the command tar --use-compress-program=zstd -xf input.tar.zstd

本数据集用于题为《面向长读长转录本定量方法的可复现模块化基准测试集》的论文。其包含模拟的牛津纳米孔测序（Oxford Nanopore Technologies, ONT）与太平洋生物科学（PacBio）测序数据集，具体如下：

小鼠PacBio与ONT数据集：

该PacBio数据集可在Zenodo记录11201284中获取。其采用Prjibelski等于2023年报道的方法进行模拟，整体错误率为1.4%。

该ONT数据集源自Zenodo记录7121404中的R10.4数据集。首先将二进制比对映射格式（Binary Alignment Map, BAM）文件转换为FASTQ格式以提取读段，随后使用BBMap工具集的shuffle.sh工具进行重排。本次模拟采用NanoSim工具完成，错误率设定为2.8%，并关闭了NanoSim默认引入背景“未比对”读段的功能，以获得更纯净的模拟数据。

ONT cDNA与直接RNA数据集（NA12878细胞系）：

这些数据集基于纳米孔全基因组测序联盟（Nanopore WGS Consortium）的NA12878样本，使用NanoSim工具模拟得到。

带有真实末端截短模式的ONT直接RNA数据集（NA12878细胞系）：

本数据集基于NA12878样本，结合DRSim与Badread工具模拟得到。其中DRSim用于模拟真实的3'端截短模式，Badread则用于模拟纳米孔测序的错误特征。更多细节可参见前述论文。

本归档文件包含运行lr_quant_benchmarks仓库相关初始基准测试所需的全部输入文件。

可使用tar归档工具与Zstandard（zstd）压缩算法，通过命令tar --use-compress-program=zstd -xf input.tar.zstd对该归档文件进行解压。