Metaphlan을 이용한 Meta genomics study #

• 배양이 불가능한 미생물을 환경에서 직접 채취하여 그 군집을 분석하여 환경과 미생물간의 상호작용을 연구

Overview #

• MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.
• MetaPhlAn relies on unique clade-specific marker genes identified from 3,000 reference genomes, allowing:
  • orders of magnitude speedups compared to existing methods;
  • unambiguous taxonomic assignments;
  • accurate estimation of organismal relative abundance;
  • species-level resolution for bacterial and archaeal organisms.

Install #

• (download : https://bitbucket.org/nsegata/metaphlan/wiki/MetaPhlAn_Pipelines_Tutorial)

   $ wget https://bitbucket.org/nsegata/metaphlan/get/default.tar.bz2
   $ tar xjvf default.tar.bz2
   $ mv *-metaphlan-* metaphlan
  

• Graph visualization (https://bitbucket.org/nsegata/graphlan/wiki/Home )

  • install

    $ hg clone https://hg@bitbucket.org/nsegata/graphlan
    

Tutorial #

Step 1 : Profiling of samples #

* input : fataq
* database 
    * 프로그램 자체내에 구축되어 있는 bacterial db
    * bowtie (BowTie2 version 2.0.0+)를 이용하기 위한 db : bowtie2db
    * blast (BLAST 2.2.25+)를 이용하기 위한 db : blastdb 
    * update : https://bitbucket.org/nsegata/metaphlan/src
* parameter 
    * multi-cpu : --nproc 5
* example
$ cat ./input/chigger | ./metaphlan.py --bowtie2db bowtie2db/mpa --bt2_ps very-sensitive --input_type multifastq > profiled_samples/chigger.txt
$ cat ./input/scutellare | ./metaphlan.py --bowtie2db bowtie2db/mpa --bt2_ps very-sensitive --input_type multifastq > profiled_samples/scutellare.txt

Step 2 : output data merging and visualization #

 $ mkdir output
 $ utils/merge_metaphlan_tables.py profiled_samples/*.txt > output/merged_abundance_table.txt

Step 3 : GraPhlAn visualization of single and multiple samples #

• heatmap

  $ mkdir output_images
  $ plotting_scripts/metaphlan_hclust_heatmap.py -c bbcry --top 25 --minv 0.1 -s log --in output/merged_abundance_table.txt --out output_images/abundance_heatmap.png
  

• graph viewing

  $ plotting_scripts/metaphlan2graphlan.py profiled_samples/chigger.txt --tree_file output_images/chigger.tree.txt --annot_file output_images/chigger.annot.txt
  $ plotting_scripts/metaphlan2graphlan.py profiled_samples/scutellare.txt --tree_file output_images/scutellare.tree.txt --annot_file output_images/scutellare.annot.txt
  $ graphlan/graphlan_annotate.py --annot output_images/chigger.annot.txt output_images/chigger.tree.txt output_images/chigger.xml
  $ graphlan/graphlan.py --dpi 200 output_images/chigger.xml output_images/chigger_circle_phylo.png
  $ graphlan/graphlan_annotate.py --annot output_images/scutellare.annot.txt output_images/scutellare.tree.txt output_images/scutellare.xml
  $ graphlan/graphlan.py --dpi 200 output_images/scutellare.xml output_images/scutellare_circle_phylo.png
  

Graph #

• example 1 profile (출처 : Biodiversity and functional genomics in the human microbiome)

• example 2 profile (출처 : Biodiversity and functional genomics in the human microbiome)

Incoming Links #

Related Bioinformaticses (Bioinformatics 0) #

• 장내 세균