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16S RNA pyrosequencing analysis


16S RNA analysis pipeline incorporates the following modules: [ trim ]-[ cdhit ]-[ mothur.align ]-[ mothur.dist ]. The pipeline web-interface includes both advanced and preconfigured settings. Advanced settings can configure each module to process data with specific settings. Most of these settings are already preconfigured with default values. If you mistakenly changed advanced setting and want to reverse them back to default you need to refresh browser ("refresh" or F5 button). The required settings include input fields required for all modules and thus must not be left empty. These include sequence file, primer length and barcodes. After starting the pipeline the process monitor will indicate which module is currently running and will report when the last has finished and data can be collected. Successful run will create a virtual folder and put all output files collected at each step into this folder. Final ‘result’ page will display the link to the generated folder where you can collect your data from.

How To Use
Please fill in the following fields: forward and [optionally] reverse primer length, barcodes with corresponding group name for each barcode. Navigate to sequence file and press ‘start‘ button. Please consult to corresponding manuals on how to twick advanced settings for the included modules. Faulty parameters may result in no output data produced.

1. trim

Advanced parameters for trim

Minimum sequence length
Maximum sequence length
Maximum presense of ambiguous bases
Maximum homopolymer length

2. Cdhit

Advanced parameters for cdhit

Word lenght
Minimal cluster size

3. Mothur.align

Advanced parameters for mothur.align

Mothur search method
Size of kmers
Align method
Reward for match
Penalty for mismatch
Penalty for gap open
Penalty for gap extend
Allow to flip

4. Mothur.dist

Advanced parameters for mothur.dist

Calculation of a distance
Penalize terminal gaps
Cutoff distance

Required fields

Forward primer length
Reverse primer length [optional, leave this emplty if there is no reverse primer]

Barcodes and group names

Alignment database to use:

Upload sequence file:
Type file name or press 'Browse' button to navigate to sequence file.

Please indicate a format of the sequence file:
xls (tab delimited text file)

File to Upload: