Phred/Phrap (sequence assembly software)
New version coming soon!
Phred
- The phred software reads DNA sequencing trace files, calls bases, and assigns a quality value to each called base
- The quality value is a log-transformed error probability
- The phred quality value have been thoroughly tested for both accuracy and power to discriminate between correct and incorrect-calls
- Phred can be use the quality values to perform sequence trimming
- Phred works well with trace files from the following manufactures' sequencing machines: Amersham Biosciences, Applied Biosystems, Beckman Instruments, and LI-COR Life Science
Phrap (Phragment assembly program)
Phrap is a program for assembling shotgun DNA sequence data. Some of its features include:
- It allows use of the entire read and not just the trimmed high quality part,
- It uses a combination of user-supplied and internally computed data quality information to improve assembly accuracy in the presence of repeats,
- It constructs the contig sequence as a mosaic of the highest quality read segments rather than a consensus,
- It provides extensive assembly information to assist in trouble shooting assembly problems,
- It handles a large amount of data sets.
Manuals