December 4, 2021 - Introduction to macro genome analysis process tools

• This article is the content of MEG gene course , Organize personal notes .
• Introduction to metagenome analysis process
  • Comparison of the advantages and disadvantages of the amplicon macrogenome
    • 16S Pros and

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    • The advantages and disadvantages of macrogenomes

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  • Analysis process

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  • The quality control
    • Two ways
      • Routine data quality control
        • More low-quality bases are removed 、N Having a certain proportion of bases reads, Remove the connector
      • Remove host contamination
        • The information from the host is eliminated by comparing with the reference genome
    • Routine quality control
      • Tool is introduced ：trimmomatic

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      • Two decouple modes

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        • Single ended mode

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        • Dual ended mode

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      • Comparison score calculation method

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      • Parameter Introduction

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    • Compare to de hosting
      • Global comparison
        • Clustal Omega、MUSCLE、HMMER, It is mainly used for multiple sequence alignment , Phylogenetic analysis , Conservative section analysis
      • Local comparison
        • Blast+、Blat、GeneWise, It is mainly used for homologous sequence analysis 、 Database comparison 、 Gene function annotation
      • Short sequence alignment
        • BWA、Bowtie2、SOAP2、TopHat、STAR、HISAT2
      • Tool is introduced ：BWA

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  • Species notes
    • Species composition
      • Based on sequence （reads） To classify
        • Analysis method
          • gene
            • Group specific genes （MetaPhlAn2）
            • Multiple universal genes （PhyloSift）
          • K-mers（kraken2）
        • Tool is introduced ：MetaPhlAn2

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        • Tool is introduced ：kraken2

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        • limitations
          • Unable to reconstruct genome and assemble
          • Depending on the choice Markers
          • Not all reads It can be used to classify species
      • Based on the sequence after splicing （contig） To classify
        • Analysis content
          • Sequence assembly （Megahit,idba）
          • Gene prediction and gene set construction （MetaGeneMark,Prodigal）
          • Species notes （NR、LCA）
          • ration （bbmap,bowtie,BWA）
        • Tool is introduced ：Megahit

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        • Genetic prediction
          • MetaGeneMark（ Fungi are recommended ）/Prodigal Conduct ORF forecast , Filter <90bp Of ORF Information ;
        • Gene set construction
          • Yes ORF Predicted results , Vegetable CD-HIT Software clustering , Get non redundant Unigenes
        • Gene abundance （ ration ）
          • bbmap, The... Of each sample CleanData Compare to Unigenes, Get the results of gene comparison reads Number and average depth
        • Species notes
          • Use non redundant gene sets , and NCBI-NR Database for homologous arm pair , Just to go LCA Algorithm , get Unigenes Species annotation information , Combined with gene abundance table , Obtain species abundance tables at different taxonomic levels
        • Functional composition

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• Introduction to common species and functional databases of macrogenomes
  • KEGG

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  • CAZy- Online comments dbCAN

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  • CARD

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• Common research ideas and analysis results in metagenomics articles

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• Macro genome Binning Introduction to theory and analysis
  • Commonly used tools
    • Recommendation tool ：MetaBAT2

      

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