<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<ANALYSIS_SET>
    <ANALYSIS analysis_center="NIID" analysis_date="2011-01-14T00:00:00+09:00" alias="DRZ000042" center_name="NIID" accession="DRZ000042">
        <TITLE>Whole genome analysis of the first reported NDM-1–producing E. coli (NDM-1 Dok01) in Japan.</TITLE>
        <STUDY_REF refname="PRJDA63849" accession="PRJDA63849">
            <IDENTIFIERS>
                <PRIMARY_ID label="BioProject ID">PRJDA63849</PRIMARY_ID>
            </IDENTIFIERS>
        </STUDY_REF>
        <DESCRIPTION>de novo assembly of 70 mer short reads of NDM-1–producing E. coli (NDM-1 Dok01) by ABySS-pe v1.2.5.
parameters: -j2 -k50 -n30 -c44.8636 -t10 -q40</DESCRIPTION>
        <ANALYSIS_TYPE>
            <DE_NOVO_ASSEMBLY>
                <PROCESSING>
                    <PIPELINE>
                        <PIPE_SECTION>
                            <STEP_INDEX>0</STEP_INDEX>
                            <PREV_STEP_INDEX>NIL</PREV_STEP_INDEX>
                            <PROGRAM>ABySS-pe</PROGRAM>
                            <VERSION>1.2.5</VERSION>
                        </PIPE_SECTION>
                    </PIPELINE>
                </PROCESSING>
            </DE_NOVO_ASSEMBLY>
        </ANALYSIS_TYPE>
        <DATA_BLOCK name="ABySS-pe assembly">
            <FILES>
                <FILE filename="NDM-1_70mer_j2k50n30c44.8636t10q40-contigs.fa" filetype="fasta" checksum_method="MD5" checksum="77a66ea2e1267b8a97c29580fa9d145a"/>
            </FILES>
        </DATA_BLOCK>
    </ANALYSIS>
    <ANALYSIS analysis_center="NIID" analysis_date="2011-03-08T00:00:00+09:00" alias="DRZ000043" center_name="NIID" accession="DRZ000043">
        <TITLE>Whole genome analysis of the DH10B strain harboring NDM-1–plasmid of E. coli (NDM-1Dok01).</TITLE>
        <STUDY_REF refname="PRJDA63849" accession="PRJDA63849">
            <IDENTIFIERS>
                <PRIMARY_ID label="BioProject ID">PRJDA63849</PRIMARY_ID>
            </IDENTIFIERS>
        </STUDY_REF>
        <DESCRIPTION>de novo assembly of 80 mer short reads of the DH10B strain harboring NDM-1–plasmid of E. coli (NDM-1Dok01) by ABySS-pe v1.2.5.
parameters: -k60 -n30 -c40 -t10 -q40 -s140</DESCRIPTION>
        <ANALYSIS_TYPE>
            <DE_NOVO_ASSEMBLY>
                <PROCESSING>
                    <PIPELINE>
                        <PIPE_SECTION>
                            <STEP_INDEX>0</STEP_INDEX>
                            <PREV_STEP_INDEX>NIL</PREV_STEP_INDEX>
                            <PROGRAM>ABySS-pe</PROGRAM>
                            <VERSION>1.2.5</VERSION>
                        </PIPE_SECTION>
                    </PIPELINE>
                </PROCESSING>
            </DE_NOVO_ASSEMBLY>
        </ANALYSIS_TYPE>
        <DATA_BLOCK name="ABySS-pe assembly">
            <FILES>
                <FILE filename="DH10B_with_NDM-1_plasmid_80mer_k60n30c40t10q40s140-contigs.fa" filetype="fasta" checksum_method="MD5" checksum="62862aac988a9f14ad6e982f37fc4891"/>
            </FILES>
        </DATA_BLOCK>
    </ANALYSIS>
</ANALYSIS_SET>
