For Customer Support contact information, and for a link to the most up-to-date version of this help, please see Before You Begin. The Phrap scores are used to determine the consensus, but are not displayed in SeqMan Pro. By contrast, SeqMan Pro enables you to assemble fragment data from small-scale sequencing projects up to tens of thousands of fragments. Once you are satisfied with your assembly, you may save your project, export the data, or merge contigs with those imported from previous assembly projects. Note that if only one trace has an intensity that is at or above threshold, the code is unambiguous A, C, G, or T.
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For each base that has sequence data only i. This topic is pgo applicable to BAM-based projects. If the codes do not agree, the base is not a putative variant.
If you prefer to assemble certain groups of sequences separately, use the Assemble in Groups option. Otherwise, if all bases in the column are identified by ambiguous codes not A, C, G, or Tand the code for the base is not the most frequently occurring, it is a putative variant base.
The C trace does not exhibit a peak. This may not be the same as the consensus called for the corresponding SeqMan Pro assembly of the same sequence data set.
By default, the primary consensus shown in the Alignment View for a Phrap assembly is the Imported Ppro consensus. If the column contains at least one unambiguous code A, C, G, or Tand the base is not the most frequently occurring unambiguous base, it is a putative variant base. See Variant Discovery Parameters for information on how pairs are used in variant discovery.
Topics and commands that are not applicable to BAM-based projects are clearly marked in this manual. If all codes do esqman agree, putative variant bases are identified in the column according to the following rules. In general, the Pro assembler should be used when your data: Lower-case consensus bases are usually called for underlying data that would not be used in a typical SeqMan Pro project due to quality trimming.
SeqMan Pro Overview
The Phred scores are for display only, and are not used in any calculations in SeqMan Pro. If it does not agree, it is a putative variant base. If Phred called four bases under a collection of peaks where the ABI base caller located only three, for prk, the Alignment View would show four bases, while the Trace Data window would show three bases.
The ambiguity code for this base is a K.
Variant Discovery Methods for SeqMan Pro Assemblies
If all codes agree, no putative variants are identified. SeqMan Pro provides two different assembly methods: The T and W bases in the column are putative variant bases and the A bases the most frequently occurring are not. SeqMan Pro is both a sequence assembler and editor for small scale sequence assemblies plasmids, PCR products, etc. The W bases in the column are putative variant bases and the K bases the most frequently occurring are not. Paired end sequence data in a Phrap assembly can be displayed in SeqMan Pro, provided data are correctly specified using the Pair Specifier parameters.
The Phrap scores are used to determine the consensus, but are not displayed in SeqMan Pro. This system evaluates the quality of the underlying trace data, and then generates the most accurate consensus sequence possible.
The Strategy View graphically summarizes the position and orientation of every constituent sequence in a contig or contig scaffold, and allows you to easily assess the coverage in your assembly.
As with all SeqMan Pro parametersyou may select one of these assemblers as your default assembly method. If the codes do not agree and one code is not encompassed by the other e.
The trace shown in the Alignment View is the same as the trace shown in the Trace Data window. This is the highest-quality base determined by Phrap, and it may not necessarily have the highest SeqMan Pro trace quality score. The T bases in the column are putative variant bases and the A bases the most frequently occurring are not.
By default, SeqMan Pro displays scores for the bases called by Phred.
Lower-case seq,an for the Phrap consensus are lower-confidence calls, and such lower-case segments of assemblies should perhaps not be used for publication. When an assembly is done by Phrap, the Phred scores are adjusted slightly to compute Phrap scores. You may also evaluate putative variants identified by SeqMan Pro.
This topic describes how SeqMan Pro identifies putative variant bases in sample sequences.