NGS_ICBR_Best-Practices (2021)

NGS_Platforms_BasicSpecs

WGA options

NGS QC-Metrics

10X Genomics-scRNAseq lib seq-recommendations

Illumina Estimating Sequencing Coverage

Illumina Index Adapters Pooling Guide

Illumina 16S metagenomics_NGS lab recomm

Illumina Sample requirements

Pooling calculator (link)

Normalization best practices (link)

Coverting ng/ul to nM for dsDNA libraries (link) 

Illumina Method Explorer (link)

Illumina Sequencing Coverage Calculator (link)

SEQUEL App Options and Seq Recommendations

ELF for PacBio library fragment size selection

PacBio IsoSeq workflow on the SEQUEL_111518

PacBio_gel-purified fragments-recommend

PacBio sample requirements

Applications Table (link)

PacBio Tutorials (link)

PacBio Video Gallery (link)

Authorship credit should be given if members of the UF ICBR NextGen DNA Sequencing staff have provided services or expertise that is critical to a manuscript. Although other circumstances may warrant authorship, authors are those that meet the items below:

• Agrees to be accountable for accuracy and/or integrity of the work and expertise. (In all our work the person executing the work takes the fullest degree of responsibility for accuracy and integrity.)
• Provides substantial contributions to the experimental design, acquisition, and analysis/interpretation of the work.
• Provides input on drafting of the work (often figures) and approves of the work to be submitted/published. (If a member of the facility has made substantial contributions it is expected that s/he will be given the opportunity to review drafts of manuscripts for accuracy/fidelity and should indicate agreement before a draft is moved forward to publication.)

If a member of UF ICBR NextGen DNA Sequencing has contributed work to a manuscript, but does not meet the criteria for authorship, the corresponding author should acknowledge the UF ICBR NextGen DNA Sequencing staff member who provided the data and their contributions should be specified.

In an effort to make acknowledgments easier than ever, UF | ICBR now offers Research Resource Identifiers (RRIDs)– persistent and unique identifiers for referencing a research resource. Copy and paste the appropriate core RRID (below) for citation. Proper acknowledgment of UF | ICBR in publications and awards validates our role in driving research forward and provides a platform to improve our services and instrumentation.

The NextGen DNA Sequencing core at the Interdisciplinary Center for Biotechnology Research (ICBR) provides researchers with quality, massively parallel, high-throughput sequencing data using the most current instrumentation, at a reasonable cost. We currently support the most popular platforms: Illumina NovaSeq X Plus, Illumina MiSeq, Illumina iSeq, PacBio SEQUEL IIe, ONT PromethION, and ONT MinION Mk1c. Together, these instruments cover a broad range of powerful applications, thus allowing biologists to investigate and obtain answers to questions that were not attainable until recently. Our free consultation services aim to help researchers navigate through the complex matrix of experimental options represented by the available sequencing technologies. Some of these important considerations include: read length, error rate, predominant type of error, data output/run, speed, cost, etc. The ever-broadening range of applications include (but are not limited to) de novo sequencing of whole genomes, targeted sequencing, transcriptome sequencing (RNA-seq), chromatin immunoprecipitation (ChIP) sequencing, methylation analysis, and metagenomics.