Segminator is a handy application that can analyze the reads from your viral data set files. The program is designed to load and analyze the information from the data generated by the 454 Life Sciences platform.
You can use this tool for identifying the variants of the viral population and remove the reads by using hamming distance cutoff thresholds.
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The output includes two files generated by the application:
– `Segminator.out`: Contains the information of the sequences and variants found in the data
– `Variants.out`: Contains the information of the variants of the data
This program is released under GNU General Public License.
While using this app you will:
– Process data sets in ‘fastq’ format.
– Identify the variants in your data.
– Get the list of reads containing the variants.
– Change the filter settings to identify the variants.
– Generate a FASTA file containing the variants identified.
Download Segmentminator:
You can download Segmentminator here:
How to Use Segmentminator:
Run Segmentminator:
1. Double click to the executable file to run it.
2. Run the application from the folder that contains both the `Segminator.out` and `Variants.out` files.
3. An option to specify which one of the output files contain the sequence names and the sequence positions will appear.
4. The application will display the output with two lists.
5. Choose one of the lists by clicking on the check boxes near the corresponding list.
6. When ‘ok’ is chosen in all the check boxes, you can save the output by clicking on the button below’save and exit’.
How to Read Segmentminator Output:
The file `Segminator.out` contains the information of the sequences and the variants found.
The columns in the following table will be generated for the output.
Column Name | Description
————— | ————————————————————————————–
– seq_id | The ids of the sequences that have been processed.
– seq_name | The name of the sequences.
– length | The length of the sequences.
– seq_pos | The position of the sequences in the file.
– seq_match | The number of copies of the specific sequence in the input.
– seq_id_threshold | An arbitrary threshold that specified the number of copies (mutations) that the sequence must have before it can be identified.
– seq_match_threshold | An arbitrary threshold that specifies the number of copies required for any variant to be identified.
This output can be converted to FASTA format by using the program FASTA format conversion
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The SegmentMinator* reads viral population from FASTQ files.
The program examines each file and identifies the reads that match a reference sequence.
It gathers and parses the relevant data from the generated FASTQ files and then outputs the statistics in a tab-delimited format.
There are few options for setting the 454 processing settings. Furthermore, the scripts are multi-platform, and run for all platforms.
After the reads are aligned and analyzed, this program extracts the interesting data and generates the output in various formats, including the statistics and html reports.
You can use this tool for identifying the variants of the viral population and remove the reads by using hamming distance cutoff thresholds.
This tool is bundled with some of the popular tools like Shifter, BaSI, JELLYFISH and many more.
This application is developed and supported by 454 Life Sciences.
Benefits:
1. Identifies the variants of the viral population
2. Finds the reads that are closer to the reference genome
3. Finds the reads that have mismatches with the reference sequence
4. Removes the reads with low allele frequency
5. Identifies the repeats and deletions in the reads
6. Creates a report and exports the data into formats like FASTA, TXT, CSV, and HTML
7. Create a version file to retrieve in the next run of the program
Program Files:
Location: C:\Program Files\454 Life Sciences\Segminator
User: Everyone
Other:
Size: –
Startup: True
What does this mean
This tool requires the following version of Java:Java Runtime Environment (JRE).
This tool requires a Microsoft Windows operating system:Windows NT, Windows 2000, Windows XP, Windows 2003, Windows 2008, Windows 7, Windows Vista, Windows 2008 Server.
This tool requires a Microsoft Windows operating system:Microsoft Windows XP Service Pack 3 (SP3) or later.
This tool requires a Microsoft Windows operating system:Microsoft Windows Vista Service Pack 1 (SP1) or later.
This tool requires the following version of Java:1.6.0_05 or later
This tool is licensed to you by 454 Life Sciences.
The license terms apply to all files associated with the software unless other terms are specifically provided in this agreement.
By installing, copying or otherwise using the software, you agree to be bound by the terms and conditions set
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Segminator’s rich output files include detailed information about both the viral particles and the host cell line. Segmentator reads are organized into contigs and singletons, allowing you to distinguish the different viral genomes.
Segminator features include:
• A customized web-based interface allowing you to quickly identify the viral variants, copy number, evolution of the population over time, and breakdown of the viral populations by categories like nuclear/cytoplasmic, and helper/killer.
• Advanced filtering options like hamming distance and sequencing quality.
• Customizable “Contigs” and “Singletons”.
• Segmentation software provides an easy way to identify both large and small variations in the sequence data. It is based on the concept of Hamming Distance, which quantifies the difference between two strings.
Segminator highly depends on the quality of the sequencing process. The longer your reads are, the more reliable is the end results. Segmentator can handle a single viral sequence length of 16KB. With read lengths less than 20KB, Segmentator will run as a standalone program.
To use the Segmentator:
• First download the program from:
• Run the Segmentator and make sure the relevant files are in the correct path.
• Start Segmentator and follow the prompts.
• When the analysis is complete, save the output and run the Segmentator again with different parameters.
• Repeat step 5 until you have covered every sub-population you are interested in.
• Export the results to any program that can read tab-delimited or csv format.
• You can also edit the analysis results and save it.
Features:
• Load the viral contigs by default. You can also filter the contigs by size range, size range, and quality range.
• Detailed statistics of the population are displayed as a table and graph.
• A copy/paste function is available to copy the results and use it as the input file for running again.
• Separate the viral contigs, cellular contigs and singletons into your own files and organize by size range, size range, and quality range.
• Generate a tab-delimited file or csv format that can be used by other software.
• An easy to use GUI that allows
What’s New in the?
Segminator is a program to analyze the data of 454 sequencing.
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