Note: Some people have been experiencing problems running jobs on the pyrosequencing pipeline. If you experience any problem please contact us and we will help you get your sequences processed.
Sequencing SSU rRNA genes from environmental samples is a standard method for determining bacterial community composition. New sequencing technologies such as pyrosequencing have been successfully used as a rapid and efficient tool to enable in-depth analysis of bacterial composition. This website provides a collection of tools to facilitate the data processing and simplify the computationally intensive analysis of such large sequencing libraries. The processed data are available in formats suitable for common ecological and statistical packages such as Spade, EstimateS and R.
We are currently developing a workbench to automate the data processing by allowing researchers to design their own complete workflow.
- Pipeline Initial Process -
sort and trim the raw reads, filter low quality sequences.
- Aligner -
align sequences using a fast, secondary-structure aware Infernal aligner.
- Alignment Merger -
merge multiple alignment files into one alignment.
- Complete Linkage Clustering -
cluster sequences by the complete-linkage clustering method.
- Dereplicate -
use this tool to make representative sequences.
- Fasta Sequence Selection -
make a sub-selection of Fasta sequences from the original sequence file.
- Spade Formatter -
make SPADE compatible input format.
- R Formatter -
make R compatible input format.
- EstimateS Formatter -
make EstimateS compatible input format.
- Shannon and Chao1 Index -
Calculate Shannon and Chao1 Index from single sample file.
- Rarefaction - Calculate Rarefaction from single sample file.
