<?xml version="1.0" encoding="UTF-8"?>
<EXPERIMENT_SET xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
  <EXPERIMENT alias="CFSAN024572_01" center_name="CFSAN" accession="SRX1051721">
    <IDENTIFIERS>
      <PRIMARY_ID>SRX1051721</PRIMARY_ID>
      <SUBMITTER_ID namespace="CFSAN">CFSAN024572_01</SUBMITTER_ID>
    </IDENTIFIERS>
    <TITLE>Whole genome shotgun sequencing of Salmonella enterica subsp. enterica serovar Newlands str. CFSAN024572 by Illumina NextSeq 500</TITLE>
    <STUDY_REF accession="SRP029479">
      <IDENTIFIERS>
        <PRIMARY_ID>SRP029479</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioProject">PRJNA217342</EXTERNAL_ID>
      </IDENTIFIERS>
    </STUDY_REF>
    <DESIGN>
      <DESIGN_DESCRIPTION>HiSeq deep shotgun sequencing of cultured isolate.</DESIGN_DESCRIPTION>
      <SAMPLE_DESCRIPTOR accession="SRS930433">
        <IDENTIFIERS>
          <PRIMARY_ID>SRS930433</PRIMARY_ID>
          <EXTERNAL_ID namespace="BioSample">SAMN03464507</EXTERNAL_ID>
        </IDENTIFIERS>
      </SAMPLE_DESCRIPTOR>
      <LIBRARY_DESCRIPTOR>
        <LIBRARY_NAME>Salmonella enterica str. CFSAN024572 shotgun</LIBRARY_NAME>
        <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
        <LIBRARY_SOURCE>GENOMIC</LIBRARY_SOURCE>
        <LIBRARY_SELECTION>RANDOM</LIBRARY_SELECTION>
        <LIBRARY_LAYOUT>
          <PAIRED NOMINAL_LENGTH="302"/>
        </LIBRARY_LAYOUT>
        <LIBRARY_CONSTRUCTION_PROTOCOL>150-bp library created for Salmonella enterica subsp. enterica serovar Newlands str. CFSAN024572.</LIBRARY_CONSTRUCTION_PROTOCOL>
      </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>101</BASE_COORD>
          </READ_SPEC>
        </SPOT_DECODE_SPEC>
      </SPOT_DESCRIPTOR>
    </DESIGN>
    <PLATFORM>
      <ILLUMINA>
        <INSTRUMENT_MODEL>NextSeq 500</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>RTA</PROGRAM>
          <VERSION>2.1.3</VERSION>
        </PIPE_SECTION>
        <PIPE_SECTION section_name="demultiplexer">
          <STEP_INDEX>1</STEP_INDEX>
          <PREV_STEP_INDEX>0</PREV_STEP_INDEX>
          <PROGRAM>bcl2fastq</PROGRAM>
          <VERSION>2.0</VERSION>
        </PIPE_SECTION>
      </PIPELINE>
    </PROCESSING>
  </EXPERIMENT>
</EXPERIMENT_SET>
