Intuitive Sequence Assembly and Editing Software
Sequence assembly combines overlapping DNA reads into longer contigs - a core task in many molecular biology workflows. CodonCode Aligner supports applications such as clone verification, PCR product analysis, mutation detection, and de novo assembly, offering precision and flexibility for both routine and complex projects. With its intuitive interface, visual and automatic editing tools, and use of quality scores, CodonCode Aligner makes it easy to detect and resolve sequencing errors, review assemblies, and produce reliable results with confidence.
Assembling Sanger Sequences with CodonCode Aligner
Assemble your sequences quickly and accurately - whether you are building separate contigs for hundreds of different clones or a single contig with thousands of sequences. CodonCode Aligner's sequence assembly features include:
- Fast assembly: Select your sequences, click a toolbar button, and get your contigs in seconds.
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Accurate consensus sequences: CodonCode Aligner uses Phred quality scores to
automatically pick the best sequence when building the consensus sequence. This can dramatically reduce the
need to edit your sequences.
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Build contigs for many clones automatically:
Assemble your contigs in groups, based on sample names.
Easily customize the way sample names are interpreted for your sequence names.
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Compare contigs: Align contigs with MUSCLE or Clustal, and go back to the
chromatograms with a simple mouse click.
- One step processing: Have your sequences automatically end clipped, vector screened, and even base called with Phred before assembly.
- Assemble cDNA to genomic sequence: Automatically align transcripts to genomic templates using large-gap alignment.
- Assemble with Phrap: Use the power of Phrap to assemble projects like whole BAC shotgun assemblies directly from CodonCode Aligner. Then, use CodonCode Aligner's contig editing tools to complete your project.
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Control:
Set assembly parameters like minimum percent identity, match scores, and
gap penalties to control the result of your assemblies.
Want to see how it works? Download a free trial, and try assembling sequences by following the step-by-step instructions in our how-to guide. Or create multiple contigs in one step, grouped by sample names, by following the how-to assemble by name guide.
NGS Assembly and Scaffolding of Bacterial Genomes
Assemble small NGS data sets like bacterial genomes quickly.
Use read pairing to scaffold contigs, and improve assembly quality
with error correction tools and external program integration.
Related Resources
FAQs about Sequence Assembly
Q: What sequence assembly and alignment algorithms does CodonCode Aligner use?
A: Since different projects require different methods to assemble or align DNA sequences, CodonCode Aligner supports a variety of different algorithms. For sequence assembly, these include:
- Global (end-to-end) alignments
- Local alignments (for unclipped sequences)
- Large gap alignments (for cDNA to genomic alignments)
- De novo NGS assemblies (for bacterial genomes and similar sized projects)
For sequence alignments, CodonCode Aligner includes various methods based on the underlying algorithms outlined above, as well as alignments with the following commonly used multiple sequence alignment programs:
- Clustal Omega (for multi-sequence alignments)
- MUSCLE (for multi-sequence alignments)
- Bowtie 2 (for short read alignments to genomes)
Q: What is the advantage of aligning contigs directly?
A: In workflows like clone verification or phylogenetic comparisons,
researchers often first assemble reads from separate clones into contigs, and
then align and compare these contigs to each other. Whereas other
DNA analysis programs typically require to create separate copies of
the "consensus" sequences for each contig, which causes
unwanted data duplication, CodonCode Aligner lets you align contigs
directly using the Compare contigs function, or the
Align with Clustal or Align with Muscle
functions.
This makes it easy to verify any observed discrepancies by going
back to the original Sanger sequence traces - just double-click on
the bases in the aligned "contig of contigs". If necessary,
sequences can be edited directly in trace or contig view, and the
edits are automatically reflected in all of the data: sequence traces,
assembled contigs, and the alignment of multiple contigs.
Q: Why is sequence assembly important?
A: Sequence assembly is essential for understanding genetic information. It enables the discovery of new genes, identification of mutations, evolutionary studies, and the development of treatments for genetic diseases.
Q: What challenges are common in sequence assembly?
A: Common challenges include handling repetitive sequences, sequencing errors, low coverage areas, and computational limitations when assembling large genomes.
Q: What is the difference between sequence assembly and sequence alignments?
A: Sequence assembly describes generating (assembling) a long DNA sequences from shorter sequences (reads). For example, to confirm the sequence of a plasmid that is several thousand base pairs long, a researcher might assemble 20 to 50 sequences that are each 500 base pairs long.
Sequence alignment describes aligning one sequence to another sequence, or multiple sequences to each other. Often, sequences are aligned to known sequences, so-called "reference sequences".
Reference-guided assembly combines aspects of both sequence assembly and sequence alignments it uses an existing known sequence (often a genome) as a template to guide the assembly.