cbcrg/dpa-analysis

Name: dpa-analysis

Owner: Notredame Lab

Description: Nextflow Pipeline for the analysis of Double Progressive Alignment (DPA)

Forked from: skptic/dpa-analysis

Created: 2017-07-11 15:15:13.0

Updated: 2017-07-11 15:15:15.0

Pushed: 2017-07-12 13:51:41.0

Homepage: null

Size: 1854

Language: Python

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README

dpa-analysis

Quick Start

Make sure you have either docker/singularity installed or the required dependencies listed in the last section.

Install the Nextflow runtime by running the following command:

$ curl -fsSL get.nextflow.io | bash

When done, you can launch the pipeline execution by entering the command shown below:

$ nextflow run skptic/dpa-analysis

By default the pipeline is executed against the provided example dataset. Check the Pipeline parameters section below to see how enter your data on the program command line.

Running Modes

There are 4 running modes which are determined based on the provided input files.

Each mode can be run with the standard MSA proceedure, with the DPA proceesure or with both (see --dpa_align and --std_align).

1: Basic Alignment Mode

Run multiple sequence alignment procedure with/without DPA.

inputs:

• sequence(s) files (FASTA) using --seqs argument

outputs:

• multiple sequence alignments (Aligned FASTA)
• guide tree(s) used for the alignment

2: Reference Alignment Mode

Run multiple sequence alignment procedure with/without DPA and score alignment against the reference alignment.

inputs:

• sequence file(s) (FASTA) using --seqs argument
• reference alignment file(s) using --refs argument

outputs:

• multiple sequence alignments (Aligned FASTA)
• tab seperated value file of alignments scored for SoP, Column and Total Column

3: Custom Guide Tree Alignment Mode

Run basic multiple sequence alignment procedure with/without DPA with user provided guide trees in Newick format.

inputs:

• sequence file(s) (FASTA) using --seqs argument
• guide tree file(s) (Newick) using --trees argument

outputs:

• multiple sequence alignments (Aligned FASTA)

4: Reference Alignment Mode with Custom Guide Tree

Run basic multiple sequence alignment procedure with/without DPA with user provided guide trees in Newick format and scored against the reference alignment.

inputs:

• sequence file(s) (FASTA) using --seqs argument
• reference alignment file(s) using --refs argument
• guide tree file(s) (Newick) using --trees argument

outputs:

• multiple sequence alignments (Aligned FASTSA)
• tab seperated value file of alignments scored for SoP, Column and Total Column

Pipeline parameters

--seqs

• Specifies the location of the input fasta file(s).
• Multiple files can be specified using the usual wildcards (*, ?), in this case make sure to surround the parameter string value by single quote characters (see the example below)
• By default it is set to the location: ./tutorial/seqs/*.fa

Example:

$ nextflow run skptic/dpa-analysis --seqs '/home/seqs/*.fasta'

This will handle each fasta file as a seperate sample.