Gene Codes Sequencher 5.4.5 For Mac
Phred and Phrap provide functions for base calling and sequence assembly, but no functions for viewing and editing assemblies. Depending on the operating system you are using, there are several choices for 'contig editors':
Operating Systems | Suggested contig editor | Alternative contig editor |
|---|---|---|
Mac OS X | CodonCode Aligner or | |
Classic MacOS | ||
Windows | Gap4 or Sequencher | |
UNIX and Linux |
Gene Codes Corporation ©2011 Sequencher 5.0 Release Notes p. 4 of 10 What’s New ALIGNING NEXT GEN SEQUENCES You can now add the alignment programs, Maq and GSNAP to Sequencher yourself and use those algorithms to align your Next Generation sequences to a reference sequence.
CodonCode Aligner
Gene Codes Sequencher for Mac 5.4.5百度网盘下载，. Sequencher for Mac OS X Sequencher 5 from Gene Codes Corporation takes you from DNA sequence data to results easier and faster than ever! Over 20 years of daily use by biologists in labs around the world have refined Sequencher’s tools and interface. Gene Codes has launched Sequencher 5.4.5., the latest version of its sequence analysis software. Sequencher® User Manual The complete software solution for sequencing DNA Windows Gene Codes Corporation.
CodonCode Aligner is a sequence assembly and contig editor program developed with the goal to offer (a) and easy-to-learn, intuitive user interface, and (b) full support for the superior algorithms provided by Phred-Phrap.
CodonCode Aligner is available for Mac OS X and Windows, and is well suited for small and medium-size projects. You can read more about Aligner, and download demo versions, at www.codoncode.com/aligner/.
Consed
Consed was developed specifically for use with Phred and Phrap. Consed offers a interactive functions as well as powerful methods for 'autofinishing' - automatic picking of additional sequence reads and walking primers to close gaps and eliminate low-quality problems in large scale sequencing projects. Consed is the tool of choice very large projects, or for high-throughput operations that can make use of Consed's 'autofinish' features.
Consed is available only for Linux and UNIX, including Mac OS X. On Mac OS X, Consed requires that X11 (freely available from Apple) is installed.
For academic users and restricted research use, Consed is available for free directly from the authors. For more information on obtaining Consed for free for restricted academic use, please visit www.phrap.org.
Consed licenses and support for unrestricted use and use at for-profit institutions are available through CodonCode. Please fill out our information request form for pricing information. You can read more about Consed at www.phrap.com/consed/
Gap4
Gap4 is part of the 'Staden package', and was developed by Rodger Staden, James Bonfield, and coworkers at the MRC Cambridge. Gap4 and the preprocessing program Phregap4 offer a number of powerful interactive features, as well as options to integrate Phred and Phrap for base calling and assembly. One potential downside is that it can take a long time to get familiar with the powerful features Gap4 offers.
Gap4 is available for UNIX, Linux, and Windows, and is free to academic users.For more information about Gap4, please visit the Staden package home page.
Sequencher
Sequencher is a popular package for Sequence assembly and editing developed by Gene Codes Corporation (no affiliation with CodonCode Corporation). The newest releases of Sequencher, version 4.1.2 and newer, can import PHRAP-generated assemblies. Even just using PHRED-generated quality scores to perform quality-based end trimming often leads to better assemblies with fewer gaps and discrepancies.
Sequencher 5.1
For larger sequencing projects with several hundred reads, for example cosmid or BAC shotgun projects, the combination of MacPHRED-MacPHRAP with Sequencher 4.1.2 can give faster and better results. In a test project with more than 800 reads, MacPHRAP assembled the project much faster and into fewer contigs then Sequencher:
MacPhrap | Sequencher 4.1.2 | |
|---|---|---|
Assembly time | 45 minutes 39 seconds (Phred quality scores used) | |
Largest contig | 17,386 bp (quality scores used) | |
# of contigs | 11 (quality scores used) |
Gene Codes Sequencher 5.4.5 For Mac Download
Sequencher assemblies were run with default setting and two different pre-processing steps.1. In one project, sequence traces without PHRED qualities were used, and ends where clipped using the default settings. This assembly led to a large number (70) of small (3,305 bp or shorter) contigs.
2. Next, the same sequences were imported with PHRED quality scores, and clipped using quality information. This assembly led to substantially fewer (11) and larger (up to 17,386 bp) contigs.
In comparison, the MacPHRAP assembly was done more than 40-fold faster, and led to only two contigs, the larger one covering most of the cosmid (44,459 bp).
Please note that importing Phrap assemblies into Sequencher can sometimes lead to 'holes' in contigs, because Sequencher may clip ends incorrectly when importing Phrap assemblies. Other potential problems and workarounds with importing Phred results into Sequencher are listed on the Sequencher trouble shooting page.
For more information about Sequencher, please visit www.genecodes.com. For more information about using PHRED quality scores in Sequencher, please visit www.codoncode.com/support/faqs/sequencher.htm
Sequencher Software
