Sequence Analysis Tools for Molecular Biologists

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Base Calling Using Phred

phred is an algorithm that takes chromatogram information from an automated sequencing run and re-evaluates the peaks to produce a "base call" that is usually significantly more accurate than the original call. In addition to recalculating the residues, phred also adds quality score information to each residue. This is a logarithmic value from 0 to 99 where a value of 10 indicates that there is a 1 in 10 chance that the call is in error, a score of 20 indicates in 1 in 100 chance the call is in error, a score of 30 indicates a 1 in 1,000 chance of an error etc. MacVector Assembler takes advantage of multi-CPU machines (such as the Intel Core Duo or multiple processor PowerPC machines) and splits up the phred jobs between the processors so that you see a speed up directly proportional to the number of processors. In addition, the phred executable is a Universal Binary, so it runs at full native speed on Intel or PowerPC processors. Once you have basecalled the imported sequences, you can view the phred base calls and the quality values by double-clicking on one of the sequences.


A trace editor window after


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Creating a Sequencing Project

Base Calling Using phred

Vector Trimming with cross_match

Assembling Sequences using phrap

Editing and Analysis of Contigs

NGS Reference Assembly using Bowtie

NGS de novo Assembly using Velvet

Comparing Assembler and AssemblyLIgn

SplitFastqFile - a ultility to break up large fastq files.

Functional comparison with Sequencher