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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: (insert basic command to generate DDV style visualization)

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

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

Result: (insert viz URL for result)

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

Command: (insert basic command to generate image-only for a FASTA file)

Result: (insert image of 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.

FASTA 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)
• Column 2. Genome A (unique)
• Column 3. Genome B (unique)
• Column 4. Genome B (gapped)

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/