SRA SARS-CoV-2检测工具

概述

SARS-CoV-2检测工具旨在快速确定未组装的NGS样本可能含有SARS-CoV-2。它作为码头中心的码头服务包提供，是在NCBI的基础上开发的SRA分类分析工具.

方法

简而言之，NCBI的Blast refseq_genomic virus数据库中包含的refseq序列补充了对经验证的病毒基因组集（RefSeq邻居）进行kmer含量分析。32公里的长度是随机的每64个碱基取样一次，并分配给原始序列的分类id。对所有序列完成此过程后，对生成的kmer进行分析，以确定它们是否与多个分类id关联。如果是，则将它们移动到最新的公共祖先节点。生成的kmer分类id对表用于分析NGS序列数据。输入数据被分解为32公里长的公里数，这些公里数被映射到滑行道；随着点击次数的增加taxid表示对样本中存在的分类群有更大的支持。虽然kmer数据库是从整个病毒超级王国构建的，严重急性呼吸系统综合征冠状病毒2型检测工具通过仅报告对冠状病毒科和相关子分类群的点击来过滤输出。输入可以是SRA登录或fasta文件。输出包括选项卡分隔格式的摘要（该*.报告文件），以及xml格式的详细结果（*.xml文件文件）。

示例用法

要测试

检索fasta分类法

输出示例

SRR11622005.报告
 
冠状病毒科100.00%（11994767次点击）
正冠状病毒95.22%（11421176次）
Betacoronavirus 95.22%（11421171次点击）
Sarbecovirus 94.63%（11351012次点击）
严重急性呼吸综合征相关冠状病毒84.99%（10194616次）
严重急性呼吸综合征冠状病毒2型55.46%（6651966次点击）

SRR11622005.xml

冠状病毒科100.00%（11994767次点击）正冠状病毒95.22%（11421176次点击）倍他冠状病毒（95.22%）（11421171次点击）Sarbecovirus 94.63%（11351012次点击）与严重急性呼吸综合征相关的冠状病毒84.99%（10194616次点击）严重急性呼吸综合症冠状病毒2 55.46%（6651966次点击。

<taxon_tree parser_version=“0.81”>
 <taxon tax_id=“1”self-count=“0”name=“root”total_count=“11994782”>
  <taxon tax_id=“10239”self-count=“14”rank=“superkind”name=“Viruses”total_count=“11994782”>分类单元tax_id=“10239”self-count=“14”rank=“superkind”name=“Viruses”total_count=“11994782”>
   <taxon tax_id=“2559587”self_count=“1”name=“Riboviria”total_count=”11994768“>
    <taxon tax_id=“76804”self-count=“0”rank=“order”name=“Nidovirales”total_count=“11994767”>
     <taxon tax_id=“2499399”self_count=“0”rank=“suborder”name=“Cornidovirineae”total_count=”11994767“>
      <taxon tax_id=“11118”self-count=“573579”rank=“family”name=“冠状病毒科”total_count=“11994767”>
       <taxon tax_id=“2501931”self_count=“0”rank=“subfamily”name=“Orthocoronavirinae”total_count=”11421176“>
        <taxon tax_id=“694002”self_count=“70131”rank=“genus”name=“Betacoronavirus”total_count=”11421171“>
         <taxon tax_id=“2509511”self_count=“1156034”rank=“subgenus”name=“萨克斯病毒”total_count=”11351012“>
          <taxon tax_id=“694009”self_count=“3542068”rank=“species”name=“严重急性呼吸综合征相关冠状病毒”total_count=”10194616“>
          <taxon tax_id=“2697049”self_count=“6651966”name=“Severe acute respiratory syndrome coronavirus 2”total_count=
          <taxon tax_id=“2709072”self_count=“358”name=“蝙蝠冠状病毒RaTG13”total_count=”358“/>
          <taxon tax_id=“1508227”self_count=“150”name=“蝙蝠SARS-like冠状病毒”total_count=”150“/>
           <taxon tax_id=“442736”self-count=“28”name=“蝙蝠SARS冠状病毒HKU3”total_count=“32”>
          <taxon tax_id=“741999”self-count=“4”name=“蝙蝠SARS冠状病毒HKU3-12”total_count=“4”/>
         </分类单元>
          <taxon tax_id=“347536”self_count=“17”name=“蝙蝠SARS冠状病毒Rm1/2004”total_count=”17“/>
          <taxon tax_id=“1283333”self_count=“9”name=“蝙蝠冠状病毒Cp/Yunnan2011”total_count=”9“/>
          <taxon tax_id=“1415852”self_count=“4”name=“蝙蝠SARS-like冠状病毒WIV1”total_count=”4“/>
          <taxon tax_id=“511429”self_count=“4”name=“SARS冠状病毒BJ182-12”total_count=”4“/>
          <taxon tax_id=“1487703”self_count=“3”name=“仿射犀牛冠状病毒”total_count=”3“/>
          <taxon tax_id=“1503302”self_count=“2”name=“BtRs-BetaCoV/HuB2013”total_count=”2“/>
          <taxon tax_id=“1503301”self_count=“2”name=“BtRs-BetaCoV/GX2013”total_count=”2“/>
          <taxon tax_id=“722424”self_count=“1”name=“SARS冠状病毒Rs_672/2006”total_count=”1“/>
         </分类单元>
         <taxon tax_id=“2720068”self_count=“0”name=“未分类的沙贝病毒”total_count=”362“>
          <taxon tax_id=“2708335”self_count=“332”rank=“species”name=“穿山甲冠状病毒”total_count=”332“/>
          <taxon tax_id=“864596”self_count=“23”rank=“species”name=“蝙蝠冠状病毒BM48-31/BGR/2008”total_count=”23“/>
          <taxon tax_id=“2591233”self_count=“6”rank=“species”name=“冠状病毒BtRl-BetaCoV/SC2018”total_count=”6“/>
          <taxon tax_id=“2591237”self_count=“1”rank=“species”name=“冠状病毒BtRs-BetaCoV/YN2018D”total_count=”1“/>
         </分类单元>
        </分类单元>
        <taxon tax_id=“2509502”self_count=“0”rank=“subgenus”name=“Nobecovirus”total_count=”22“>
        <taxon tax_id=“694006”self_count=“22”rank=“species”name=“Rousettus bat冠状病毒HKU9”total_count=”22“/>
        </分类单元>
        <taxon tax_id=“696098”self_count=“0”name=“未分类Betacoronavirus”total_count=”3“>
          <taxon tax_id=“663565”self_count=“2”rank=“species”name=“蝙蝠SARS冠状病毒Rs806/2006”total_count=”2“/>
          <taxon tax_id=“1117224”self-count=“1”rank=“species”name=“蝙蝠冠状病毒2265/菲律宾/2010”total_count=“1”/>
        </分类单元>
        <taxon tax_id=“2509494”self_count=“3”rank=“subgenus”name=“Merbecovirus”total_count=”3“/>
       </分类单元>
       <taxon tax_id=“693996”self_count=“0”rank=“genus”name=“α冠状病毒”total_count=”5“>
        <taxon tax_id=“2509514”self_count=“0”rank=“subgenus”name=“Tegacovirus”total_count=”5“>
        <taxon tax_id=“693997”self_count=“5”rank=“species”name=“α冠状病毒1”total_count=”5“/>
      </分类单元>
     </分类单元>
    </分类单元>
    <taxon tax_id=“693995”self_count=“0”rank=“subfamily”name=“冠状病毒亚科”total_count=”12“>
     <taxon tax_id=“2664420”self_count=“0”name=“未分类冠状病毒”total_count=“12”>
      <taxon tax_id=“1881090”self_count=“7”rank=“species”name=“单核犀牛冠状病毒”total_count=”7“/>
      <taxon tax_id=“1508220”self_count=“5”rank=“species”name=“蝙蝠冠状病毒”total_count=”5“/>
     </分类单元>
    </分类单元>
   </分类单元>
  </分类单元>
  </分类单元>
 </分类单元>
</分类单元>
</分类单元>
</taxon_tree>

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