GenoREAD
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Application data |
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| Created by | Wilson M, Cai Y |
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| Biological application domain(s) | Sequencing, Clone verification |
| Principal bioinformatics method(s) | Read mapping, Sequence assembly, Sequence alignment |
| Technology | Sanger |
| Created at | Virginia Bioinformatics Institute, Virginia Tech |
| Maintained? | Yes |
| Input format(s) | FASTA, AB1, Excel |
| Output format(s) | HTML, JPG, ZIP, .txt |
| Programming language(s) | Perl, PHP, JavaScript |
| Software libraries | MIRA, phred, crossmatch |
| Operating system(s) | Linux 64 |
| Contact: | jpeccoud@vbi.vt.edu |
Summary: GenoREAD is a web-based, sequence verification software that can be used to compare Sanger sequencing trace files against a reference sequence. Users can either submit their sequencing results one clone at a time, or they can submit a series of clones (as a project) to run at once. Results can be viewed online or downloaded.
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Description
Sequence verification – the process of comparing the physical sequence of a clone to a known reference sequence – is a critical quality control step in gene synthesis. This is typically achieved by aligning one trace file to the reference sequence and relying on the operator to detect the possible presence of mutations. This approach is labor-intensive. It does not scale up well to projects requiring the verification of many plasmids. In cases where the reference sequence does not match the sequencing data or two different trace files do not match one another, there is a serious possibility of human errors. GenoREAD is a web-based application that addresses these issues. It provides a front end to a finely tuned data analysis pipeline that has been validated by comparing the results of the automatic analysis to the manual review of thousands of sequencing datasets.
Links
References
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