RDP's Pyrosequencing Pipeline: aka Molecular Biology Toolkit Repository

Pipeline Initial Process

Initial processing steps include sorting the raw reads into those from each of the original samples, trimming off the key tag and primers, and removing sequences of low quality. The primers are not limited to V4 primers. Reverse primers are optional. More help is available here.

The IDs in the FASTA file and the quality file must match. If your FASTA and quality file have an header with additional description such as "uaccno=someid", then the ID after "uaccno=" it will be considered as an ID for that sequence and printed the same when outputting the result, otherwise the name after the ">" sign will be considered as an ID.

Email Address (optional):
Sequence File in FASTA or SFF Format:
Quality File in FASTA Format (optional):
Upload a tag file (optional): (tag file?)
Gene Name:(Why ?)	16S rRNA Other
Forward Primers1: one primer per line. primer length < 64 bases.
1Refers to the gene-targeting primer region, excluding sequencing adaptor or multiplexing tag, at the proximal end of the sequencing process
Reverse Primers2: one primer per line. primer length < 64 bases.
2Refers to the gene-targeting primer region, excluding sequencing adaptor or multiplexing tag, at the distal end of the sequencing process

FILTERS:
Forward primer max edit distance (0 to 2):		Reverse primer max edit distance (0 to 2):
Max number of N's:		Min sequence length (>=50):
Minimum Average Exp Quality Score:		Keep primers: