cbcrg/regressive-msa repository overview

⁠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.

⁠Alignment Methods

The following alignment methods are available.

⁠Tree Building Methods

⁠Containers

All the methods above are available in a Docker⁠ image on DockerHub here⁠ and the image is tested to be compatible with the Singularity⁠.

The container also contains test data consisting of protein sequences, reference alignments and trees in the directory /test_data.

To launch the container interactively with Docker run:

docker run cbcrg/regressive-msa

To launch the container interactivly with Singularity run:

singularity shell docker://cbcrg/regressive-msa

⁠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.