Note: If you experience problems with the pyrosequencing pipeline, please contact us and we will help you get your sequences processed.

News Items

Jun09: Released myRDP SRA Prepkit Beta to help prepare and manage the documents required for submitting Pyrosequencing data to Short Read Archive.

May09: Added distance matrix tools that can be used with Mothur. Aligner now checks sequence orientation for those who wish to use it with sequences not run through our Initial Processing step.

April09: All tools that require file uploads now support the following compressed file extensions: .zip, .gz, .bz2, .tar, .tgz, .tbz or .tbz2, .tar.gz, .tar.bz2

Multiple files of the same type can be combined into a single archive if the tool requires multiple files (Aligner, Dereplication, AlignmentMerger, etc.)

All pyro pipeline result files are downloaded in .tgz format to support results larger than 2GB.

The Ribosomal Database Project's Pyrosequencing Pipeline aims to simplify the processing of large 16s rRNA sequence libraries obtained through pyrosequencing. This site processes and converts the data to formats suitable for common ecological and statistical packages such as SPADE, EstimateS, and R.

Data Processing Steps:

• Pipeline Initial Process - sort and trim the raw reads, filter low quality sequences.
  
• Aligner - align sequences using the fast, secondary-structure aware Infernal aligner.
  
• Complete Linkage Clustering - cluster sequences by the complete-linkage clustering method.
  

Formats for Common Programs:

• SPADE Formatter - make a SPADE compatible input format.
  
• R Formatter - make a R compatible input format.
  
• EstimateS Formatter - make an EstimateS compatible input format. Can also be used with PAST.
  
• Mothur: Column Distance Matrix - create a column distance matrix compatible with Mothur.
  
• Mothur: Phylip Distance Matrix - create a matrix and sample group file compatible with Mothur's LIBSHUFF function.
  

Analysis Tools:

• Shannon & Chao1 Index - calculate Shannon Index & Chao1 estimator from a single sample file.
  
• Rarefaction - calculate Rarefaction from a single sample file.
• RDP Classifier - assign 16S rRNA sequences to our taxonomical hierarchy.
• RDP LibCompare - compare two sequence libraries using the RDP Classifier.

NCBI/EBI Short Read Archive Submission Tools:

• myRDP SRA Prepkit Beta - helps prepare and manage the complicated xml documents required for submitting your Pyrosequencing data to NCBI and EBI's Short Read Archive.
  
• Fastq - A java web start program that creates a Fastq file from a fasta and quality file. Requires Java 5 or above.
  

Miscellaneous Utilities:

• Alignment Merger - merge multiple alignment files into one alignment.
  
• Dereplicate - use this tool to make representative sequences.
  
• FASTA Sequence Selection - make a sub-selection of FASTA sequences from the original sequence file.