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Josiah Seaman edited this page Apr 3, 2018 · 42 revisions

FluentDNA User Documentation

Introduction

FluentDNA is a multi-platform command-line tool for generating visualizations of DNA data.

Generating visualizations

After you have the software installed (insert link to installation instructions), the command line is used to generate visualizations that are accessible through a localhost web browser or a local image viewer. First, launch the FluentDNA server using fluentdna.py --runserver This will make all your results available at http://127.0.0.1:8000

Simple FASTA file (DNA)

Generating a basic visualization of a FASTA file downloaded from NCBI or another source is accomplished with the following commands:

Command: fluentdna.py --fasta="example_data/hg38_chr19_sample.fa" --outname="Test Simple"

This generates an image pyramid with the standard legend (insert image of legend) and nucleotide number display.

For example, the data file in <site-packages>/DDV/example_data/example_data/hg38_chr19_sample.fa

Result: Hg38 chr19 sample

It is also possible to generate an image file only that can be accessed with an image viewer using --no_webpage.

**Command: **fluentdna.py --fasta="example_data/hg38_chr19_sample.fa" --outname="Test Simple" --no_webpage

Result: Example FluentDNA output of Human Chr19 2MBp

Multi-part FASTA file (DNA)

Multi-part FASTA format includes multiple sequences in the same file. A sequence record in a FASTA format consists of a single-line description (sequence name), followed by line(s) of sequence data. The first character of the description line is a greater-than (">") symbol. Multi-part format Example:

>seq0
AATGCCA
>seq1
GCCCTAT

The following command generates a multi-part FASTA file visualization:

For example, the following data file: "<site-packages>/DDV/example_data/example_data/Human selenoproteins.fa" **Command: **fluentdna.py --fasta="example_data/Human selenoproteins.fa" Result: Human Selenoproteins

This generates a multi-scale image of the multi-part FASTA file. Note that if you don't specify --outname= it will default to the name of the FASTA file.

Using this simple command, FluentDNA can visualize an entire draft genome at once.
Result: Ash Tree Genome (Fraxinus excelsior)

Additional options - see also:

  • --outname
  • --sort_contigs
  • --no_titles
  • --natural_colors
  • --base_width

Alignment of two Genomes

This generates an alignment visualization of two genomes (A and B):

Command: (insert command to generate)

This generates a multi-scale image of the alignment. There are 4 columns in this visualization:

  • Column 1. Genome A (gapped entire DNA of genome A)
  • Column 2. Genome A (unique DNA of A)
  • Column 3. Genome B (unique DNA of B)
  • Column 4. Genome B (gapped entire DNA of genome B)

For example, the following data file: (insert data file link)

Result: https://dnaskittle.com/ddvresults/dnadata/Parallel_hg38_and_panTro5_chr19/

Multiple Sequence Alignment Families

This generates a visualization of a multiple alignment data file (from BLAST?)

Command: (insert command to generate)

This generates a multi-scale image of the multiple alignment. The multiple alignment results are sorted by gene name.

For example, the following data file: (insert data file link)

Result: https://dnaskittle.com/ddvresults/dnadata/Fraxinus%20Homologous%20Gene%20Groups/

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