NTContent is a sliding window based tool used to assess the evolution of the percentage of specific nucleotides along a DNA/RNA sequence.
The input is a DNA/RNA sequence in fasta format.
The output is a tab-delimited text file showing for each window its central position and the percentage of the desired nucleotides.
Additionally, a gnuplot script can be created with the -p option.
- gcc
- zlib
$ make
$ NTContent [options] sequence.fasta| Option | Description |
|---|---|
| -o FILE | File output. Default: stdout |
| -w INT | Window Size. Default: Sequence length / 25 |
| -s INT | Step. Default: Window Size / 10 |
| -n STR | Nucleotide(s) to look for [ACGTUWSMKRYBDHVNZ]. Default: GC |
| -r STR | Region of interest [FROM:TO] |
| -p | Create a gnuplot script |
| -d | Combine 'samtools depth' results with NTContent in the gnuplot script |
| -h | Help |
$ NTContent -n GC -w 50 -s 10 hiv.fasta > GC.txt(...)
25 54.00
35 56.00
45 56.00
55 52.00
65 48.00
75 48.00
85 46.00
95 46.00
105 52.00
115 48.00
125 52.00
135 48.00
145 46.00
155 42.00
165 54.00
175 54.00
185 54.00
195 56.00
205 60.00
(...)
Aurélien Guy-Duché
- Issue Tracker: https://github.com/guyduche/NTContent/issues
- Source Code: https://github.com/guyduche/NTContent
The project is licensed under the MIT2 license.