Difference between revisions of "PGAP"
(→Step 3 Running PGAP) |
|||
| (2 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
= Introduction = | = Introduction = | ||
| + | |||
| + | A perl based pipeline for clustering genes and ascertaining pan-genomes of prokaryotes. | ||
= Usage = | = Usage = | ||
| − | + | '''PGAP.pl''' is the principle executable. Typing it without any arguments will give a helpful output. | |
== Step 3 Running PGAP == | == Step 3 Running PGAP == | ||
For PAGP, there are five functional modules: | For PAGP, there are five functional modules: | ||
| − | * functional genes into clusters | + | * functional genes into clusters (invoked on commandline via '''--cluster''') |
| − | * ascertain pan-genome profile | + | * ascertain pan-genome profile (invoked on commandline via '''--pangenome''') |
| − | * genetic variation of functional genes | + | * genetic variation of functional genes (invoked on commandline via '''--variation''') |
| − | * species evolution analysis | + | * species evolution analysis (invoked on commandline via '''--evolution''') |
| − | * function enrichment of gene clusters | + | * function enrichment of gene clusters (invoked on commandline via '''--function''') |
Example command for this stage: | Example command for this stage: | ||
The following commands trigger all these analysis modules with the default parameters. | The following commands trigger all these analysis modules with the default parameters. | ||
| − | PGAP.pl -strains nickname1+...+nicknameN -input <input_dir> -output <out_dir> --cluster -pangenome --variation --evolution --function -method MP | + | PGAP.pl -strains nickname1+...+nicknameN -input <input_dir> -output <out_dir> --cluster --pangenome --variation --evolution --function -method MP|GF |
| + | |||
| + | Notes: | ||
| + | * The main options have single dash options: 1) '''-strains''' 2) '''-input''' 3) '''-output''' 4) '''-method''' | ||
| + | * The five modules can be run separately or collectively | ||
| + | * a '''--thread''' for setting the number of option is avilable | ||
Latest revision as of 17:52, 6 May 2016
Introduction
A perl based pipeline for clustering genes and ascertaining pan-genomes of prokaryotes.
Usage
PGAP.pl is the principle executable. Typing it without any arguments will give a helpful output.
Step 3 Running PGAP
For PAGP, there are five functional modules:
- functional genes into clusters (invoked on commandline via --cluster)
- ascertain pan-genome profile (invoked on commandline via --pangenome)
- genetic variation of functional genes (invoked on commandline via --variation)
- species evolution analysis (invoked on commandline via --evolution)
- function enrichment of gene clusters (invoked on commandline via --function)
Example command for this stage:
The following commands trigger all these analysis modules with the default parameters.
PGAP.pl -strains nickname1+...+nicknameN -input <input_dir> -output <out_dir> --cluster --pangenome --variation --evolution --function -method MP|GF
Notes:
- The main options have single dash options: 1) -strains 2) -input 3) -output 4) -method
- The five modules can be run separately or collectively
- a --thread for setting the number of option is avilable
