Sequence Analysis Tools for Molecular Biologists

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Creating a Sequencing Project

The first step in any assembly is to create a project and import the sequences/trace files that are to be assembled. MacVector Assembler lets you directly import files in the following formats;

Chromatogram Files

• ABI (from 373, 377, 3700 and 3730 models)

• SCF version 2

• SCF version 3


Sequence Files

• MacVector

• FastA

• FastQ

Sequence files in other formats should first be converted into a compatible format using MacVector.

The imported sequences are maintained in a project window where you can sort and rename etc.


A populated sequence assembly project


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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