Metadata XML examples

Experiment (Spot, Platform)

The DRA metadata web tool nor excel cannot describe technical reads (adapter, primer and barcode sequences). When sequencing data contain technical reads to be submitted, submitters need to create Experiment XML files and describe technical reads in the <SPOT_DESCRIPTOR>.

454 single reads

Read composition

Read Index :	0	1
Read :	TCAG	ATAGAGTTGATCCTGGCTCAT……………
Base Coordinate :	1	5 80
Read Type :	Adapter	Forward

Spot (Read Spec) metadata

Read Index	Read Class	Read Type	Ordering Method
0	Technical Read	Adapter	BaseCoord = 1
1	Application Read	Forward	BaseCoord = 5

Experiment XML (SPOT_DESCRIPTOR)

<SPOT_DESCRIPTOR>
  <SPOT_DECODE_SPEC>
    <READ_SPEC>
      <READ_INDEX>0</READ_INDEX>
      <READ_CLASS>Technical Read</READ_CLASS>
      <READ_TYPE>Adapter</READ_TYPE>
      <BASE_COORD>1</BASE_COORD>
    </READ_SPEC>
    <READ_SPEC>
      <READ_INDEX>1</READ_INDEX>
      <READ_CLASS>Application Read</READ_CLASS>
      <READ_TYPE>Forward</READ_TYPE>
      <BASE_COORD>5</BASE_COORD>
    </READ_SPEC>
  </SPOT_DECODE_SPEC>
</SPOT_DESCRIPTOR>

454 paired reads

Read composition

Read Index :	0	1	2	3
Read :	TCAG	ATAGAGT……………CCTGG	TCGTAT……………TATTACG	CTCAT……………
Base Coordinate :	1	5
Read Type :	Adapter	Forward	Linker	Forward

Spot (Read Spec) metadata

Read Index	Read Class	Read Type	Ordering Method
0	Technical Read	Adapter	BaseCoord = 1
1	Application Read	Forward	BaseCoord = 5
2	Technical Read	Linker	ExpectedBasecallTable
3	Application Read	Forward	RelativeOrder

Expected Basecall Table

Base Call	Min Match	Max Mismatch	Match Edge
TCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTACG	38	5	full
CGTAATAACTTCGTATAGCATACATTATACGAAGTTATACGA	38	5	full

Experiment XML (SPOT_DESCRIPTOR)

<SPOT_DESCRIPTOR>
  <SPOT_DECODE_SPEC>
    <READ_SPEC>
      <READ_INDEX>0</READ_INDEX>
      <READ_CLASS>Technical Read</READ_CLASS>
      <READ_TYPE>Adapter</READ_TYPE>
      <BASE_COORD>1</BASE_COORD>
    </READ_SPEC>
    <READ_SPEC>
      <READ_INDEX>1</READ_INDEX>
      <READ_CLASS>Application Read</READ_CLASS>
      <READ_TYPE>Forward</READ_TYPE>
      <BASE_COORD>5</BASE_COORD>
    </READ_SPEC>
    <READ_SPEC>
      <READ_INDEX>2</READ_INDEX>
      <READ_CLASS>Technical Read</READ_CLASS>
      <READ_TYPE>Linker</READ_TYPE>
      <EXPECTED_BASECALL_TABLE>
        <BASECALL min_match="38" max_mismatch="5" match_edge="full">TCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTACG</BASECALL>
        <BASECALL min_match="38" max_mismatch="5" match_edge="full">CGTAATAACTTCGTATAGCATACATTATACGAAGTTATACGA</BASECALL>
      </EXPECTED_BASECALL_TABLE>          
    </READ_SPEC>   
    <READ_SPEC>
      <READ_INDEX>3</READ_INDEX>
      <READ_CLASS>Application Read</READ_CLASS>
      <READ_TYPE>Forward</READ_TYPE>
      <RELATIVE_ORDER follows_read_index="2"/>
    </READ_SPEC>        
  </SPOT_DECODE_SPEC>      
</SPOT_DESCRIPTOR>

Experiment (Pipeline)

Examples of describing pipelines (series of program for analysis).

Example 1 of Experiment XML Pipeline

<PROCESSING>
  <PIPELINE>
    <PIPE_SECTION section_name="Base Caller">
      <STEP_INDEX>1</STEP_INDEX>
      <PREV_STEP_INDEX>NIL</PREV_STEP_INDEX>
      <PROGRAM>Casava</PROGRAM>
      <VERSION>V1.8.3_V3.2.1</VERSION>
      <NOTES/>
    </PIPE_SECTION>
    <PIPE_SECTION section_name="Quality Scores">
      <STEP_INDEX>2</STEP_INDEX>
      <PREV_STEP_INDEX>1</PREV_STEP_INDEX>
      <PROGRAM>Casava</PROGRAM>
      <VERSION>V1.8.3_V3.2.1</VERSION>
      <NOTES/>
    </PIPE_SECTION>
  </PIPELINE>
</PROCESSING>

Example 2 of Experiment XML Pipeline

<PROCESSING>
  <PIPELINE>
    <PIPE_SECTION>
      <STEP_INDEX>1</STEP_INDEX>
      <PREV_STEP_INDEX/>
      <PROGRAM>bwa</PROGRAM>
      <VERSION>0.5.9-r16</VERSION>
      <NOTES>BWA-MEM algorithm alignment</NOTES>
    </PIPE_SECTION>
    <PIPE_SECTION>
      <STEP_INDEX>2</STEP_INDEX>
      <PREV_STEP_INDEX>1</PREV_STEP_INDEX>
      <PROGRAM>Picard</PROGRAM>
      <VERSION>1.74(1243)</VERSION>
      <NOTES>Duplicate reads marked</NOTES>
    </PIPE_SECTION>
    <PIPE_SECTION>
      <STEP_INDEX>3</STEP_INDEX>
      <PREV_STEP_INDEX>2</PREV_STEP_INDEX>
      <PROGRAM>GATK</PROGRAM>
      <VERSION>1.4-29</VERSION>
      <NOTES>Indel realignment</NOTES>
    </PIPE_SECTION>
    <PIPE_SECTION>
      <STEP_INDEX>4</STEP_INDEX>
      <PREV_STEP_INDEX>3</PREV_STEP_INDEX>
      <PROGRAM>GATK</PROGRAM>
      <VERSION>1.4-29</VERSION>
      <NOTES>Base quality score recalibration</NOTES>
    </PIPE_SECTION>
  </PIPELINE>
</PROCESSING>