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