Simulated metagenomic DNA sequencing reads for complete FDA-ARGOS bacterial genomes

This dataset comprises simulated DNA sequencing reads in FASTQ format for all 988 complete FDA-ARGOS bacterial reference genomes (https://www.nature.com/articles/s41467-019-11306-6) including plasmids, downloaded on 2025-02-25. Included are simulated long Oxford Nanopore Technologies R10.4 reads with ~4% error rate and simulated short (2x150bp) Illumina reads with 1% error rate. The source reference sequences are provided as argos988.fa.zst. Files are compressed with Zstandard in order to fit inside Zenodo's 50GB limit. Simulated long reads (Oxford Nanopore Technologies) argos988.fastq.zst Measured empirical error rate: ~4% Simulator: PBSIM 3.0.4 (https://academic.oup.com/nargab/article/4/4/lqac092/6855700) Model: ERRHMM-ONT-HQ Depth: 10x Mean read length: 5,000bp Max read length: 50,000bp Mean accuracy: 0.98 Random seed: 1 Command used: for fasta in argos988/*.fa; do acc=$(basename "$fasta" .fa) pbsim --seed 1 --strategy wgs --method errhmm --errhmm pbsim3/data/ERRHMM-ONT-HQ.model --depth 10 --genome ${fasta} --prefix ${acc} --id-prefix ${acc}__ --length-mean 5000 --length-max 50000 --accuracy-mean 0.98; cat ${acc}*.fastq | pigz > ${acc}.fastq.gzdone Simulated short reads (Illumina) argos988.r1.fastq.zst and argos988.r2.fastq.zst Measured empirical error rate: 1% Simulator: dwgsim 0.1.14; conda package version 1.1.14, (https://github.com/nh13/DWGSIM) Read length: 2x150bp (paired) Depth: 10x Random read probability (-y): 0 Error rate (-e and -E): 0.01 Mutation rate (-r): 0.0 Of which low frequency somatic mutations (-F): 0.0 Random seed (-z): 1 Command used: for fasta in argos988/*.fa; do acc=$(basename "$fasta" .fa) dwgsim -C 10 -1 150 -2 150 -y 0.0 -o 1 -z 1 -F 0.0 -r 0.0 -e 0.01 -E 0.01 "$fasta" "$acc"done本数据集包含针对全部988个完整FDA-ARGOS细菌参考基因组（包含质粒）的FASTQ格式（FASTQ）模拟DNA测序读段，下载于2025年2月25日，相关参考文献见https://www.nature.com/articles/s41467-019-11306-6。数据集包含错误率约4%的模拟牛津纳米孔技术（Oxford Nanopore Technologies）R10.4长读段，以及错误率1%的2×150bp Illumina短读段。源参考序列以argos988.fa.zst格式提供，所有文件均采用Zstandard（Zstandard）压缩，以适配Zenodo（Zenodo）的50GB存储限制。 模拟长读段（牛津纳米孔技术） 数据文件：argos988.fastq.zst 实测经验错误率：约4% 模拟器：PBSIM 3.0.4（相关文献见https://academic.oup.com/nargab/article/4/4/lqac092/6855700） 模型：ERRHMM-ONT-HQ 测序深度：10x 平均读长：5000bp 最大读长：50000bp 平均准确率：0.98 随机种子：1 使用命令： for fasta in argos988/*.fa; do acc=$(basename "$fasta" .fa) pbsim --seed 1 --strategy wgs --method errhmm --errhmm pbsim3/data/ERRHMM-ONT-HQ.model --depth 10 --genome ${fasta} --prefix ${acc} --id-prefix ${acc}__ --length-mean 5000 --length-max 50000 --accuracy-mean 0.98; cat ${acc}*.fastq | pigz > ${acc}.fastq.gzdone 模拟短读段（Illumina） 数据文件：argos988.r1.fastq.zst与argos988.r2.fastq.zst 实测经验错误率：1% 模拟器：dwgsim 0.1.14；conda包版本为1.1.14（相关仓库见https://github.com/nh13/DWGSIM） 读长：2×150bp（双端测序） 测序深度：10x 随机读段概率（参数-y）：0 错误率（参数-e与-E）：0.01 突变率（参数-r）：0.0 低频体细胞突变比例（参数-F）：0.0 随机种子（参数-z）：1 使用命令： for fasta in argos988/*.fa; do acc=$(basename "$fasta" .fa) dwgsim -C 10 -1 150 -2 150 -y 0.0 -o 1 -z 1 -F 0.0 -r 0.0 -e 0.01 -E 0.01 "$fasta" "$acc"done