Flower

Flower extracts flow values from SFF (Standard Flowgram Format) files produced by Roche 454 sequencing and converts them into textual formats to enable base calling, quality assessment, and error-probability analysis.

Key Features:

• Flow value extraction: Reads SFF files and extracts embedded flow values used for interpreting sequencing signal intensities.
• Binary SFF parsing: Parses the compact, binary SFF file structure generated by Roche 454 sequencing technology.
• Output format conversion: Converts extracted SFF contents into textual formats, including tab-delimited text and other user-specified formats.
• Support for base calling and quality assessment: Provides flow-value data that inform base calling and estimation of sequencing error probabilities.

Scientific Applications:

• Metagenomics: Enables use of flow-value information from 454 reads to improve reliability of sequence-based community analyses.
• Base calling and read quality assessment: Supplies flow values for evaluating read quality and informing base-calling decisions.
• Data integration: Facilitates conversion of 454 SFF data into tab-delimited or other textual formats for downstream bioinformatics tools and analyses.

Methodology:

Flower reads compact, binary SFF files produced by Roche 454, extracts the embedded flow values, and converts them into user-specified textual formats (e.g., tab-delimited text).