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Usage-env01-anvio-7.1.md

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This page introduces the usages in the environment of 'anvio-7.1'.

Updated on 2023-08-02

Usage description

Usage text

  # annotation
  (environment) ~/location$ command line

Move to your workplace and activate the environment first

  # don't forget to change to your directory first
  (base) jiang@azur:~$ cd user_name
  
  # check the current enviroment at the beginning of the command line, like the 'base' here
  (base) jiang@azur:~/user_name$
  # if not the target environment, activate it by 'conda activate'
  (base) jiang@azur:~/user_name$ conda activate anvio-7.1
  # check again at the beginning, now it is 'anvio-7.1', good to go
  (anvio-7.1) jiang@azur:~/user_name$

Let's start !!!

Here I mainly introduce the three usages:

  • Pangenomic
  • Metagenomics
  • Meta-pan genomics

Usage01: Pangenomics

01-00: EASY WAY - Using Jiang's script

One script for easy use of pangenome database preparation was written.

USAGE: xxx/00-scripts/script_CJ_pangenomics_workflow_full_Ver6.sh GENOME_DIR RUN_NAME NUM_THREADS

This is the workflow for Pangenomic analyses, written by Chunqi Jiang. If you have any questions, please let him know. Following steps are included

  1. Simplify the contigs names in your fasta file
  2. Create a contigs database for each genome
  3. HMM decoration for each contigs database
  4. COG annotations for each contigs database
  5. Kofam annotation for each contigs database
  6. Generate an anvio genomes storage including all databases
  7. Run the pangenome analysis (--use-ncbi-blast --enforce-hierarchical-clustering)
  8. Perform an additional ANI calculation"

Before starting: put all your genomes (.fna) in a directory, such as '00-GENOMES'

Please limit the name characters to ASCII letters, digits, and the underscore

# check everything is ready
(anvio-7.1) jiang@azur:~/user_name/your_place$ ls
   00-GENOMES 
# start script
(anvio-7.1) jiang@azur:~/user_name/your_place$ ~/user_jiang/00-scripts/script_CJ_pangenomics_workflow_full_Ver7.sh GENOME_DIR RUN_NAME NUM_THREADS
	# example
	(anvio-7.1) jiang@azur:~/user_name/your_place$ ~/user_jiang/00-scripts/script_CJ_pangenomics_workflow_full_Ver7.sh 00-GENOMES Test_Jiang 20

That's it! Easy right?

GENOME_DIR: the directory containing all your genome files;

RUN_NAME: your project name, anything is ok;

NUM_THREADS: number of threads you want to use, usually recommend 20 here.

01-01: HARD BUT WORTH - Step by Step

Checking your input FASTA files
## Re-formatting your input FASTA (simplify the header lines of FASTA files for genomes)
# one cmd for all (multiple files)
(anvio-7.1) jiang@azur:~/user_name/your_place$ for f in *.fasta; do anvi-script-reformat-fasta $f -o ../01_SIMPLIFY/${f%.*}_simplify.fasta -l 0 --simplify-names --seq-type NT ; done

# one by one (one file per time) if you like

01-02 Converting FASTA files into anvi’o contigs databases

## Creating the anvi’o contigs databases
# one cmd for all (multiple files)
(anvio-7.1) jiang@azur:~/user_name/your_place$ for f in *_headfix.fasta; do anvi-gen-contigs-database -f $f -o CD_${f%_*}_CD.db; done
# one by one if you like


## Annotating your contigs databases
# anvi-run-hmms
(anvio-7.1) jiang@azur:~/user_name/your_place$ for f in *_CD.db; do anvi-run-hmms -c $f -T n; done (n: the highest sequence number)
# anvi-run-ncbi-cogs (COG20)
(anvio-7.1) jiang@azur:~/user_name/your_place$ for f in *_CD.db; do anvi-run-ncbi-cogs -c $f -T 20; done
# Run KOfam HMMs
(anvio-7.1) jiang@azur:~/user_name/your_place$ for f in *_CD.db; do anvi-run-kegg-kofams -c $f -T 20; done

01-03 Generating an anvio genomes storage

#external_database_path.txt name contigs_db_path

(anvio-7.1) jiang@azur:~/user_name/your_place$ anvi-gen-genomes-storage -e external_database_path.txt -o GDB_XXXX_GENOMES.db

01-04 Running the pangenome analysis

# slow mode, but recommend
(anvio-7.1) jiang@azur:~/user_name/your_place$ anvi-pan-genome -g GDB_XXXX_GENOMES.db -n PROJECT_XXXX -T 20 --enforce-hierarchical-clustering --use-ncbi-blast
# fast mode
(anvio-7.1) jiang@azur:~/user_name/your_place$ anvi-pan-genome -g GDB_XXXX_GENOMES.db -n PROJECT_XXXX -T 20 --enforce-hierarchical-clustering

--use-ncbi-blast (default: False) This program uses DIAMOND by default;

--enforce-hierarchical-clustering (default: False)/--skip-hierarchical-clustering (default: False)

01-05 Displaying the pangenome

# before displaying remotely, re-connect the server by 'ssh -L 8080:localhost:8080 xxxx'
(anvio-7.1) jiang@azur:~/user_name/your_place$ anvi-display-pan -p PROJECT_XXXX/PROJECT_XXXX-PAN.db -g G_XXXX_GENOMES.db --server-only -P 8080

01-06 Default summary

 # check collections
 (anvio-7.1) jiang@azur:~/user_name/your_place$ anvi-summarize  -p PROJECT_XXXX/PROJECT_XXXX-PAN.db -g G_XXXX_GENOMES.db --list-collections
 # add a 'DEFAULT' collection for pangenome
 (anvio-7.1) jiang@azur:~/user_name/your_place$ anvi-script-add-default-collection  -p PROJECT_XXXX/PROJECT_XXXX-PAN.db 
 # summarize the 'DEFAULT' collection
 (anvio-7.1) jiang@azur:~/user_name/your_place$ anvi-summarize -p PROJECT_XXXX/PROJECT_XXXX-PAN.db -g G_XXXX_GENOMES.db  -C DEFAULT -o SUMMARY-XXXX-default

01-07 Optional choice

 #  ANI calculation
(anvio-7.1) jiang@azur:~/user_name/your_place$ anvi-compute-genome-similarity --program pyANI -i txt-internal-genomes.txt -p PROJECT-Sulfitobacter-PAN/PROJECT-Sulfitobacter-PAN-PAN.db -o pyANI-ANIb -T 20

Usage02: Metagenomics

Usage03: Meta-pan genomics