MINSEQE: Minimum Information about a high-throughput Nucleotide SeQuencing Experiment - a proposal for standards in functional genomic data reporting

MINSEQE describes the Minimum Information about a high-throughput nucleotide SEQuencing Experiment that is needed to enable the unambiguous interpretation and facilitate reproduction of the results of the experiment. By analogy to the MIAME guidelines for microarray experiments, adherence to the MINSEQE guidelines will improve integration of multiple experiments across different modalities, thereby maximising the value of high-throughput research. 

The five elements of experimental description considered essential when making data available supporting published high-throughput sequencing experiments are as follows:

1. The description of the biological system, samples, and the experimental variables being studied:
   • “compound” and “dose” in dose-response experiments or “antibody” in ChIP-Seq experiments, the organism, tissue, and the  treatment(s) applied.
2. The sequence read data for each assay:
   • read sequences and base-level quality scores for each assay; FASTQ format is recommended, with a description of the scale used for quality scores.
3. The ‘final’ processed (or summary) data for the set of assays in the study:
   • the data on which the conclusions in the related publication are based, and descriptions of the data format.
4. General information about the experiment and sample-data relationships:
   • a summary of the experiment and its goals, contact information, any associated publication, and a table specifying sample-data relationships.
5. Essential experimental and data processing protocols:
   • how the nucleic acid samples were isolated, purified and processed prior to sequencing, a summary of the instrumentation used, library preparation strategy, labelling and amplification methodologies, alignment algorithms and data filtering plus data processing & analysis protocols.

The present document contains version 1.0 of the MINSEQE guidelines, which originated from discussions at an FGED-organized workshop held in Berkeley in March 2008.