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':
- Oct 13, 2016 Gene Codes announces the release of Sequencher 5.4. This new release adds features to Sanger, NGS and RNA-Seq analyses such as: Expanded Cufflinks suite with the addition of Cuffquant and Cuffnorm. Sequencher 5.4 also has replicates functionality with a unique Conditions and Replicates Editor for Cuffdiff and Cuffnorm.
- Gene Codes Sequencher 5.4.5 For Mac DNA 序列分析 英文版(蘋果電腦專用)Gene Codes Sequencher 5.4.5 For.
- 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.
- The Sequencher software will be found in StartAll ProgramsGene CodesSequencher 5.4. When you launch the software, a dialog box will come up that gives you License Options. Choose “I have a license file,” “Next.” Download the license key file here: SequencherKey.lic (right click to save).
Operating Systems | Suggested contig editor | Alternative contig editor |
---|---|---|
Mac OS X | CodonCode Aligner or (for larger projects) Consed | |
Classic MacOS | ||
Windows | Gap4 or Sequencher | |
UNIX and Linux |
Gene Codes releases Sequencher 5.4.6. Gene Codees announces CodeLinker 1.0. Gene Codes releases Sequencher 5.4.5. Gene Codes releases Sequencher 5.4.1. Gene Codes releases Sequencher 5.4. This new release adds features to Sanger, NGS and RNA-Seq analyses. Sequencher 5.3 introduces new functionality for RNA-Seq analyses, as well as.
CodonCode Aligner
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.
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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.
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) |
Sequencher assemblies were run with default setting and two different pre-processing steps.
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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).
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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
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 (for larger projects) Consed | |
Classic MacOS | ||
Windows | Gap4 or Sequencher | |
UNIX and Linux |
CodonCode Aligner
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/.
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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.
![Mac Mac](/uploads/1/1/7/8/117825072/722355380.png)
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/
Gene Codes Sequencher 5.4.5 For Mac Free
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.
Gene Codes Sequencher 5.4.5 For Mac Os
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.
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) |
Sequencher 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.
Gene Codes Sequencher 5.4.5 For Macbook Pro
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.
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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