Published September 17, 2022
| Version v3
Dataset
Open
LMAS Test Dataset - ZymoBIOMICS Microbial Community Standards
Authors/Creators
- 1. Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
Description
The eight bacterial genomes and four plasmids of the ZymoBIOMICS Microbial Community Standards were used as reference. It contains tripled complete sequences for the following species:
- Bacillus subtilis
- Enterococcus faecalis
- Escherichia coli
- Escherichia coli plasmid
- Lactobacillus fermentum
- Listeria monocytogenes
- Pseudomonas aeruginosa
- Salmonella enterica
- Staphylococcus aureus
- Staphylococcus aureus plasmid 1
- Staphylococcus aureus plasmid 2
- Staphylococcus aureus plasmid 3
It also downloads the raw sequence data of the mock communities, with an even and logarithmic distribution of species:
- ERR2984773 - Evenly distributed real sample
- ERR2935805 - Log distributed real sample
A set of simulated samples were generated from the genomes in the ZymoBIOMICS standard though the InSilicoSeq sequence simulator (version 1.5.2), including both even and logarithmic distribution, with and without Illumina error model. The number of read pairs generated matches the number of read pairs in the real data for each distribution. The following samples are available in Zenodo:
- ENN - Evenly distributed sample with no error model
- EMS - Evenly distributed sample with Illumina MiSeq error model
- LNN - Log distributed sample with no error model
- LHS - Log distributed sample with Illumina HiSeq error model