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SRA Handbook [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2010-.

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SRA Handbook [Internet].

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SRA Glossary

Created: ; Last Update: May 20, 2011.

1. Overview

This document lists terms and usage for SRA XML. Each set of terms is associated with a “descriptor,” which packages like concepts together into computable text data that can be expressed as XML.

2. Sample Descriptor

The sample descriptor captures information that would allow the user of the SRA to map the sequencing data to a single sample, or a sample pool member.

See Table 1 for sample descriptor terms.

Table 1

Table 1

– Sample Descriptor Terms

3. Library Descriptor

The library descriptor captures information that would allow the user of the SRA to interpret the sequencing data’s origin and preparation.

See Table 2 for library descriptor terms.

Table 2

Table 2

- Library Descriptor Terms

4. Spot Descriptor

The spot descriptor captures information that would allow the user of the SRA to interpret the sequencing data and differentiate between technical and application extents in the read. Reads that are mate pairs are concatenated into a single monolithic “spot” sequence.

See Table 3 for spot descriptor terms.

Table 3

Table 3

- Spot Descriptor Terms

5. Gap Descriptor

The gap descriptor captures information that would allow the user of the SRA to map the sequencing data to a putative reference genome substrate and to understand mate pairing statistics.

See Table 4 for gap descriptor terms.

Table 4

Table 4

- Gap Descriptor Terms

6. Platform Descriptor

The platform descriptor captures information about the instrument that produced the sequencing data.

See Table 5 for platform descriptor terms.

Table 5

Table 5

- Platform Descriptor Terms

7. Processing Descriptor

The processing descriptor captures information about the treatment of the data after the sequencing instrument produced it, prior to submission to the SRA.

See Table 6 for processing descriptor terms.

Table 6

Table 6

- Processing Descriptor Terms

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