Then, use CodonCode Aligner's contig editing tools to complete your project. Assemble with Phrap: Use the power of Phrap to assemble projects like whole BAC shotgun assemblies directly from CodonCode Aligner.Aligner's support for NGS error correction and assembly programs can easily be adapted to allow use of different programs. If you use the popular Sequencher sequence assembly program from Genecodes you cannot run the current version of Sequencher 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. Error correct NGS reads before assembly to get larger contigs and scaffolds. Assemble small NGS data sets like bacterial genomes quickly, and have CodonCode Aligner use information from read pairs to generate scaffolds. Assemble and scaffold bacterial genomes. Sequencher will automatically compare the forward and the reverse-complement orientations to assemble the best possible contigs, so you can assemble DNA.If reads assemble into two or more contigs then a Collection. In Map view all aligned reads will be depicted above the consensus. The initial sequence (labelled Original Sequence in Sequence view) in the file is the consensus created by the CAP3 assembler. contig assembly, and custom reporting that is superior in nature to those. One step processing: Have your sequences automatically end clipped, vector screened, and even base called with Phred before assembly. The new sequence file opens with the Alignment side panel displayed. Accuracy is greater than 99 using Phred 20 bi-directional sequence traces.Compare contigs: Align contigs with MUSCLE or Clustal, and go back to the chromatograms with a simple mouse click.Easily customize the way sample names are interpreted for your sequence names. Build contigs for many clones automatically: Assemble your contigs in groups, based on sample names. Optimize for More dissimilar sequences (discontiguous megablast) Optimize for Somewhat similar sequences (blastn) Choose a BLAST algorithm Help.
This can dramatically reduce the need to edit your sequences. Accurate consensus sequences: CodonCode Aligner uses Phred quality scores to automatically pick the best sequence when building the consensus sequence.
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