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FluentDNA User Documentation

Introduction

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

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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.

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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-libs>/DDV/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:

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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:

Command: (insert command to generate multi-part FASTA file visualization)

This generates a multi-scale image of the multi-part FASTA file.

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

Result: https://dnaskittle.com/ddvresults/dnadata/Ash%20Tree%20Genome%20-%20BATG-0_5/

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Alignment of two Genomes

This generates an alignment visualiazation 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/

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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/