<?xml version="1.0" encoding="UTF-8"?>
<EXPERIMENT_SET xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
  <EXPERIMENT alias="Salmonella Montevideo str. CT_02035320 Experiment" center_name="CFSAN" accession="SRX105769">
    <IDENTIFIERS>
      <PRIMARY_ID>SRX105769</PRIMARY_ID>
      <SUBMITTER_ID namespace="CFSAN">Salmonella Montevideo str. CT_02035320 Experiment</SUBMITTER_ID>
    </IDENTIFIERS>
    <TITLE>Whole genome sequencing of Salmonella Montevideo str. CT_02035320 by 454 GS FLX</TITLE>
    <STUDY_REF accession="SRP009357">
      <IDENTIFIERS>
        <PRIMARY_ID>SRP009357</PRIMARY_ID>
        <SUBMITTER_ID namespace="CFSAN">Salmonella Montevideo str. CT_02035320</SUBMITTER_ID>
      </IDENTIFIERS>
    </STUDY_REF>
    <DESIGN>
      <DESIGN_DESCRIPTION>454 GS FLX fragment library kit</DESIGN_DESCRIPTION>
      <SAMPLE_DESCRIPTOR accession="SRS270923">
        <IDENTIFIERS>
          <PRIMARY_ID>SRS270923</PRIMARY_ID>
          <SUBMITTER_ID namespace="CFSAN">FDA230</SUBMITTER_ID>
        </IDENTIFIERS>
      </SAMPLE_DESCRIPTOR>
      <LIBRARY_DESCRIPTOR>
        <LIBRARY_NAME>Salmonella Montevideo str. CT_02035320 shotgun</LIBRARY_NAME>
        <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
        <LIBRARY_SOURCE>GENOMIC</LIBRARY_SOURCE>
        <LIBRARY_SELECTION>RANDOM</LIBRARY_SELECTION>
        <LIBRARY_LAYOUT>
          <SINGLE/>
        </LIBRARY_LAYOUT>
      </LIBRARY_DESCRIPTOR>
      <SPOT_DESCRIPTOR>
        <SPOT_DECODE_SPEC>
          <SPOT_LENGTH>0</SPOT_LENGTH>
          <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>
    </DESIGN>
    <PLATFORM>
      <LS454>
        <INSTRUMENT_MODEL>454 GS FLX</INSTRUMENT_MODEL>
      </LS454>
    </PLATFORM>
    <PROCESSING>
      <PIPELINE>
        <PIPE_SECTION section_name="base caller">
          <STEP_INDEX>0</STEP_INDEX>
          <PREV_STEP_INDEX>NULL</PREV_STEP_INDEX>
          <PROGRAM>454 Data Acquisition</PROGRAM>
          <VERSION>2.3</VERSION>
        </PIPE_SECTION>
      </PIPELINE>
    </PROCESSING>
  </EXPERIMENT>
  <EXPERIMENT alias="Iron Torrent resequencing on Salmonella Montevideo CT_02035320" center_name="CFSAN" accession="SRX119990">
    <IDENTIFIERS>
      <PRIMARY_ID>SRX119990</PRIMARY_ID>
      <SUBMITTER_ID namespace="CFSAN">Iron Torrent resequencing on Salmonella Montevideo CT_02035320</SUBMITTER_ID>
    </IDENTIFIERS>
    <TITLE>Whole genome sequencing of Salmonella Montevideo str. CT_02035320 by ION_TORRENT</TITLE>
    <STUDY_REF accession="SRP009357">
      <IDENTIFIERS>
        <PRIMARY_ID>SRP009357</PRIMARY_ID>
        <SUBMITTER_ID namespace="CFSAN">Salmonella Montevideo str. CT_02035320</SUBMITTER_ID>
      </IDENTIFIERS>
    </STUDY_REF>
    <DESIGN>
      <DESIGN_DESCRIPTION>Ion Torrent fragment library kit III</DESIGN_DESCRIPTION>
      <SAMPLE_DESCRIPTOR accession="SRS270923">
        <IDENTIFIERS>
          <PRIMARY_ID>SRS270923</PRIMARY_ID>
          <SUBMITTER_ID namespace="CFSAN">FDA230</SUBMITTER_ID>
        </IDENTIFIERS>
      </SAMPLE_DESCRIPTOR>
      <LIBRARY_DESCRIPTOR>
        <LIBRARY_NAME>Salmonella Montevideo str. CT_02035320 shotgun</LIBRARY_NAME>
        <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
        <LIBRARY_SOURCE>GENOMIC</LIBRARY_SOURCE>
        <LIBRARY_SELECTION>RANDOM</LIBRARY_SELECTION>
        <LIBRARY_LAYOUT>
          <SINGLE/>
        </LIBRARY_LAYOUT>
      </LIBRARY_DESCRIPTOR>
      <SPOT_DESCRIPTOR>
        <SPOT_DECODE_SPEC>
          <SPOT_LENGTH>0</SPOT_LENGTH>
          <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>
    </DESIGN>
    <PLATFORM>
      <ION_TORRENT>
        <INSTRUMENT_MODEL>Ion Torrent PGM</INSTRUMENT_MODEL>
      </ION_TORRENT>
    </PLATFORM>
    <PROCESSING>
      <PIPELINE>
        <PIPE_SECTION section_name="base caller">
          <STEP_INDEX>0</STEP_INDEX>
          <PREV_STEP_INDEX>NULL</PREV_STEP_INDEX>
          <PROGRAM>Torrent_suite</PROGRAM>
          <VERSION>1.5.1/2.0</VERSION>
        </PIPE_SECTION>
      </PIPELINE>
    </PROCESSING>
    <EXPERIMENT_ATTRIBUTES>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>chip_model</TAG>
        <VALUE>316</VALUE>
      </EXPERIMENT_ATTRIBUTE>
    </EXPERIMENT_ATTRIBUTES>
  </EXPERIMENT>
  <EXPERIMENT alias="cross-platform validation study on FDA1015 Montevideo CT_02035320 by MiSeq" center_name="CFSAN" accession="SRX149554">
    <IDENTIFIERS>
      <PRIMARY_ID>SRX149554</PRIMARY_ID>
      <SUBMITTER_ID namespace="CFSAN">cross-platform validation study on FDA1015 Montevideo CT_02035320 by MiSeq</SUBMITTER_ID>
    </IDENTIFIERS>
    <TITLE>Whole genome sequencing of Salmonella Montevideo str. CT_02035320 by MiSeq</TITLE>
    <STUDY_REF accession="SRP009357">
      <IDENTIFIERS>
        <PRIMARY_ID>SRP009357</PRIMARY_ID>
        <SUBMITTER_ID namespace="CFSAN">Salmonella Montevideo str. CT_02035320</SUBMITTER_ID>
      </IDENTIFIERS>
    </STUDY_REF>
    <DESIGN>
      <DESIGN_DESCRIPTION>Illumina Nextera index kit</DESIGN_DESCRIPTION>
      <SAMPLE_DESCRIPTOR accession="SRS270923">
        <IDENTIFIERS>
          <PRIMARY_ID>SRS270923</PRIMARY_ID>
          <SUBMITTER_ID namespace="CFSAN">FDA230</SUBMITTER_ID>
        </IDENTIFIERS>
      </SAMPLE_DESCRIPTOR>
      <LIBRARY_DESCRIPTOR>
        <LIBRARY_NAME>Salmonella Montevideo str. CT_02035320 shotgun</LIBRARY_NAME>
        <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
        <LIBRARY_SOURCE>GENOMIC</LIBRARY_SOURCE>
        <LIBRARY_SELECTION>RANDOM</LIBRARY_SELECTION>
        <LIBRARY_LAYOUT>
          <PAIRED NOMINAL_LENGTH="300"/>
        </LIBRARY_LAYOUT>
      </LIBRARY_DESCRIPTOR>
      <SPOT_DESCRIPTOR>
        <SPOT_DECODE_SPEC>
          <SPOT_LENGTH>302</SPOT_LENGTH>
          <READ_SPEC>
            <READ_INDEX>0</READ_INDEX>
            <READ_CLASS>Application Read</READ_CLASS>
            <READ_TYPE>Forward</READ_TYPE>
            <BASE_COORD>1</BASE_COORD>
          </READ_SPEC>
          <READ_SPEC>
            <READ_INDEX>1</READ_INDEX>
            <READ_CLASS>Application Read</READ_CLASS>
            <READ_TYPE>Reverse</READ_TYPE>
            <BASE_COORD>152</BASE_COORD>
          </READ_SPEC>
        </SPOT_DECODE_SPEC>
      </SPOT_DESCRIPTOR>
    </DESIGN>
    <PLATFORM>
      <ILLUMINA>
        <INSTRUMENT_MODEL>Illumina MiSeq</INSTRUMENT_MODEL>
      </ILLUMINA>
    </PLATFORM>
    <PROCESSING>
      <PIPELINE>
        <PIPE_SECTION section_name="base caller">
          <STEP_INDEX>0</STEP_INDEX>
          <PREV_STEP_INDEX>NULL</PREV_STEP_INDEX>
          <PROGRAM>GAPipeline</PROGRAM>
          <VERSION>RTA1.13.46</VERSION>
        </PIPE_SECTION>
      </PIPELINE>
    </PROCESSING>
  </EXPERIMENT>
</EXPERIMENT_SET>
