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Comparing MacVector with Assembler with Sequencher

"Sequencher is not optimized for your Mac"

If you use the popular Sequencher sequence assembly program from Genecodes and have recently updated your operating system to MacOS 10.13.4, you may have encountered the following dialog;

SequencherPerformanceWarning

The root of this problem is that Sequencher 5.4.6 (the latest version for the Mac) is a 32-bit application and is particularly reliant on an ancient "Carbon" OS 9-compatibility framework that Apple has been telling developers for many years will be phased out in the near future. It appears that day is finally arriving and this warning dialog is the first indication that Apple will shortly make good on that promise. It is highly likely that Sequencher will be unable to run on one of the macOS releases in the next year or so.

MacVector with Assembler has been fully 64-bit for many years (since MacVector 13) and has no dependency on the "Carbon" framework. It provides almost all of the functionality of Sequencher within an updated modern interface, along with a host of additional functionality and integration with all of the DNA analysis tools within the core MacVector application.

For a limited time, we are offering a 50% discount to all Sequencher users who wish to upgrade to MacVector with Assembler. There are more details here.

Project Interface

Like Sequencher, MacVector with Assembler provides a simple Project-oriented interface where you can import and drag and drop files for Assembly. Unlike Sequencher, MacVector lets you have multiple projects open at one time.

SequencherProject

A typical Sequencher Project window

Assemblerproject

A similar project in MacVector + Assembler

Viewing and Editing Contigs

Sequencher uses two coordinated windows to displaythe contig alignment and any associated chromatogram files;

Sequenchercontig

The Sequencher Contig Editor (note the use of two windows)

MacVector displays the information in two panes in a single window, along with (optionally) quality information. Unlike Sequencher, trimmed bases are not deleted, but are simply shown greyed out. A unique "Dots" mode (not shown) replaces residues that match the consensus with a dot so that your eyes are immediately drawn to SNPs and other mismatches.

Assemblercontig

The MacVector with Assembler Contig Editor

Comparison of MacVector with Assembler and Sequencher Functionality

While not every Sequencher function and feature is present in MacVector with Assembler and MacVector provides many additional sequence analysis functions that are not present in Sequencher, the two applications are broadly similar when it comes to de novo and reference-based assembly capabilities. The table below list the major features present in the two programs;

MacVector with Assembler

Sequencher

Assembles ABI Data

Yes

Yes

Assembles NGS Data

Yes

Yes

Simple Project Interface

Yes

Yes

de novo Assembly

Phrap, Velvet, SPAdes

Sequencher, Velvet

Base calling with Quality Values

Phred

Sequencher

Reference Assembly

Bowtie, MacVector

Sequencher, BWA, GSNAP, Maq

Built-in Reference Assembly Editor/Viewer

Yes

Requires external Tablet viewer

Supports Quality Values

Yes (standard phred values)

Yes (Sequencher)

SNP Detection

Yes

Yes

Multiple Sequence Alignment

ClustalW, MUSCLE, T-Coffee

ClustalW, MUSCLE

Restriction Enzyme mapping

Extensive

Minimal

Variant calling with SAMtools

Yes

Yes

Multiplex ID

No

Yes

Modern graphical interface

Yes

No

High quality vector-based graphical export

Yes

No

64-bit

Yes

No

Compatible with future macOS releases

Yes

No

Scan fasta/q files and retrieve matches

Yes

No

Built-in NCBI BLAST

Yes

No

Extensive DNA analysis and editing tools

Yes

No

Save unaligned reads to separate file(s)

Yes

No

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Overview

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