Data from Readsynth: short-read simulation for consideration of composition-biases in reduced metagenome sequencing approaches

Background
The application of reduced metagenomic sequencing approaches holds promise as a middle ground between targeted amplicon sequencing and whole metagenome sequencing approaches but has not been widely adopted as a technique. A major barrier to adoption is the lack of read simulation software built to handle characteristic features of these novel approaches. Reduced metagenomic sequencing (RMS) produces unique patterns of fragmentation per genome that are sensitive to restriction enzyme choice, and the non-uniform size selection of these fragments may introduce novel challenges to taxonomic assignment as well as relative abundance estimates.
Results
Through the development and application of simulation software, readsynth, we compare simulated metagenomic sequencing libraries with existing RMS data to assess the influence of multiple library preparation and sequencing steps on downstream analytical results. Based on read depth per position, readsynth achieved 0.79 Pearson’s corre..., Sequence data were collected and aggregated from publicly available NCBI SRA databases for raw sequence data (https://www.ncbi.nlm.nih.gov/sra) and NCBI RefSeq databases for reference genome assemblies (https://www.ncbi.nlm.nih.gov/refseq/).
Downloaded reference genomes have been concatenated and indexed using command line \"cat\" command and the bwa index command., , # readsynth\_analysis

[https://doi.org/10.5061/dryad.nzs7h44zk](https://doi.org/10.5061/dryad.nzs7h44zk)

The dataset contained here provides the necessary raw sequence data to perform analyses for the simulation software [readsynth](https://github.com/ryandkuster/readsynth).

The dataset includes the genomes and databases necessary to reproduce the steps in the github repository [readsynth_analysis](https://github.com/ryandkuster/readsynth_analysis) and correspond with that repository's \"raw_data\" directory.

## Description of the data and file structure

The genome directory \"raw_data\" is broken into the following subdirectories (further descriptions below):

```
.
├── helius
│   └── all_2084
│   ├── genomes
│   └── genomes_combined
├── kraken_dbs
│   ├── k2_pluspfp_20220607
│   ├── snipen_bei_db
│   │   └── library
│   │   └── added
│   └── sun_atcc_db
│   └── library
│   └── added
├── liu_RMS
│   └── mock_community_estimate
│   ├── 10M_bracken_profile
│ ...