Phred Phrap Consed Cross match

Phred Phrap Consed Cross match performs base-calling, sequence assembly, sequence comparison, and automated finishing to produce high-confidence DNA sequence data for shotgun and other sequencing projects.

Key Features:

• Phred: Performs base-calling from DNA sequencing trace files and assigns quality values and error probabilities to each called base.
• Phrap: Assembles shotgun DNA sequences into contigs using Phred quality scores to prioritize high-confidence reads.
• Cross_match: Uses a banded version of SWAT to compare two sets of DNA sequences and identify similarities and differences.
• Consed/Autofinish: Uses error probabilities from Phred and Phrap to identify contaminant reads, unremoved vector sequences, chimeric or deleted reads, suggest directed sequencing reads and specialized techniques, and automate finishing and gap-closure decisions.

Scientific Applications:

• Shotgun sequencing projects: Provides integrated base-calling, quality-aware assembly, and automated finishing for large-scale shotgun workflows.
• cDNA sequencing: Supplies base quality scoring and assembly functionality applicable to cDNA sequencing studies.
• Whole bacterial genome projects: Enables assembly and finishing of bacterial genomes using quality-informed contig construction and automated finishing.
• Comparative sequence analysis and contaminant detection: Performs sequence comparisons and assists in detecting contaminants and vector sequences.

Methodology:

Phred performs base-calling from sequencing trace files and assigns quality scores used by Phrap to assemble reads into contigs; Cross_match applies a banded SWAT for sequence comparisons; Consed/Autofinish uses error probabilities to locate contaminants, vector sequences, chimeric or deleted reads, suggest directed sequencing reads and techniques, and automate gap closure and finishing decisions.