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Chromatogram & Sequence Assembly Tools

  • Phred Phrap System
The phred software reads DNA sequencing trace files, calls bases, and assigns a quality value to each called base. phred/Phrap package is the most popular software to process chromatograms generated from sequencing project. In this package, phred is the base-caller that retrieves the sequence information and gives every base a quality value, named "phd value"; phrap is the assembler that helps scientists to assemble sequence fragments into contigs or singlets. After running phred, the sequences retrieved from chromatograms need to be trimmed based on phd values and the vector sequences used for cloning before they are sent to Phrap for assembly, though people have different protocols on how to do the quality and vector trimming. Phrap is a program for assembling shotgun DNA sequence data. Phrap authors are planning to add EST sequence assembly feature to the next version of phraps. Currently, we do not recommend phrap used as the assembler for EST sequences although many people do it.

  • Transcript Assembler
TranscriptAssembler is the standard program to assembly EST sequences. It is a complete, high-capacity solution for EST-based transcript reconstruction. TranscriptAssembler provides a comprehensive pipeline for all of the steps required to accurately filter, mask, cluster, and assemble transcripts. In addition to sequence assembling, TranscriptAssembler supports alternative splice form detection, chimera detection, and user-friendly visualization as well. It's very easy to construct various assembly pipeline for sequences from different species, or for different purposes.