Questions WGSTranscriptomics 0002

1. Sample Quantities and Library Preparation

Could you please clarify the anticipated sample batch sizes? Specifically, should vendors expect to receive batches of approximately 65 individual samples, or will the samples require multiple replicate library preparations? If replicates are required, how many library preparations should be anticipated per sample?
Sample batch sizes will vary based on project needs and will likely range between 15-65 samples. Depending on project need, we may decide to sequence replicates for a select group of samples per run (i.e. 2-10 samples)

2. WGS and RNA-seq Sequencing Depth

Could you please clarify the expected sequencing depth for each service? •

Whole Genome Sequencing (WGS): How many sequencing reads or read pairs are required per sample?
At minimum, we would aim for 150-300 M paired-end reads for PE150 reads. That number would adjust depending on target genome size and paired-end read length. Depth must be sufficient for species/strain identification and antimicrobial resistance gene detection.

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RNA Sequencing (RNA-seq): How many sequencing reads or read pairs are required per sample?
For RNA-seq, our requirements will vary based on projects and whether they are focused on gene expression profiling or metatranscriptomics. We would likely aim for 10-20 M informative reads from 30-50 M raw reads/sample for transcriptomics. In the past, we have sequenced PE100.

Additionally, are there specific requirements for read length and single-end versus pairedend sequencing? For WGS, we will consider both PE150 and PE250. We do not typically use single-end sequencing.
For RNA-seq, we will consider single-end (for gene expression profiling) and both singleand paired-end (for gene expression and transcriptome analysis). If these requirements vary by project, could you please advise what assumptions vendors should use when preparing their pricing?

Most of our sequencing needs stem from assessing potential metabolic function and/or gene expression of mixed microbial communities from freshwater and soil environments. We are typically most interested in species/strain identification, antimicrobial resistance and virulence gene pathways, nutrient cycling, and biodegradation.