Installing Bioinformatics Software-metaphlan2

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Last week 20161021-20161028 of the task is not finished, so today to pits (smiling face)

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This article references: https://bitbucket.org/biobakery/biobakery/wiki/metaphlan2

METAPHLAN2 is a tool for depicting microbial community composition using the macro genome bird marksmanship sequencing data.

PS: Representation of diagrams related to system development

Installation:

1. Download and unzip 2. Modify/etc/profile, add path 3. Direct use of metaphlan2.py

4. Use this command to give the Bowtie2 path --bowtie2_exe<bowtie2>.

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Help information: metaphlan2.py -H | Less use the UP and down arrows to scroll to see, Q exits.

Experimental content:

Step 0: Download data (right-click, copy link address)

mkdir mytest

CD mytest

wget https://bitbucket.org/biobakery/biobakery/raw/tip/demos/biobakery_demos/data/metaphlan2/input/ Srs014459-stool.fasta.gz

Step 1: Use a single reads file as input

 metaphlan2. PY srs014476-supragingival_plaque. Fasta. GZ --input_type fasta >  Srs014476-supragingival_plaque_profile. TXT 
 
  bowtie2out.txt :  intermediate mapping results to unique sequence markers 
 You can use this command to view (but I think with gedit also can ah = = unless it is the command line) 
 Less -s  Srs014476-supragingival_plaque.fasta.gz.bowtie2out.txt 
    profile.txt : Final result 
  

 < span class= "n" >  explanation: 
 1. This is the description of the classification:  kingdom:k__, phylum:p__, class:c__, order:o__, family:f__, genus:g__, species:s__   
  2. The number is the percentage Br>3. OTU equivalents can be extracted by using only the species-level   s__   clades from this file (again, Making 
 sure to include clades unclassified at the level). 
 
 Step 2: Multithreading--nproc commands 
             

 metaphlan2. PY srs014459-stool. Fasta. GZ --input_type fasta --nproc Span class= "Mi" >4 > srs014459-stool_profile< Span class= "O". txt               

 < span class= "n" >  
 Step 3: Multiple input processing 
   

 for f in *. Fasta. Gzdo metaphlan2. PY $f --input_type fasta --nproc 4 > ${< span class= "n" >f%. Fasta. Gz}_profile. Txtdone 
 
 Step 4: Merge results (using utils/merge_metaphlan_tables.py script) 
      

/home/pxy7896/downloads/metaphlan2/utils/merge_metaphlan_tables.py *_profile.txt > Merged_abundance_table.txt

Can be viewed with LibreOffice calc ... Because of the number of data, a little ugly. For example, the preceding is the classification information, followed by a number of file information.

Step 5: Visualization of data, heatmap

(1) Installing brew

sudo apt install linuxbrew-wrapper

(2) Installation Hclust2

Brew Tap biobakery/biobakery

Brew Install hclust2

Installation failed ... The problem is weird ... So I decided to install the R Language Pack first, using the function heatmap inside to draw.

Installation R See:

(3) Generation of species species abundance table (only at the species level)

Use command: grep -E "(s__) | ( ^id) "Merged_abundance_table.txt | grep- V "t__" | sed ' s/^.*s__//g ' > Merged_abundance_table_species.txt

Command explanation:

1. grep is a software (library) output in the specified mode, refer to the user manual:http://www.gnu.org/software/grep/manual/grep.pdf

2.

 < span class= "n" > < Span class= "Err" >      

Installing bioinformatics Software-metaphlan2