Sanger Sequence Assembly Software

SANGER SEQUENCE ASSEMBLY

The most accurate sequence assembly software for Sanger data, with easy-to-use features for removing contaminants, trimming, viewing chromatograms, evaluating coverage, and identifying variants

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Be confident in the accuracy of your assembly.

Assembling your sequencing data is one of the most critical steps in DNA sequencing because accuracy is so important. The assembly algorithm we use in our Sanger sequence assembly software has been proven to be the most accurate on the market for Sanger ABI sequencing data. When compared to the competition, our algorithm does the best job assembling sequences into a single contig, and calling the most accurate consensus sequence based on trace quality and shape. Following assembly, SeqMan Ultra uniquely offers you the ability to easily edit your assembled data – exposing or trimming ends, introducing mutations – as well as analyzing your assembled data, including viewing chromatograms, evaluating coverage and analyzing variants. Getting it right matters. Use the sequence assembly tools in SeqMan Ultra and be confident in the accuracy of your assembly.

Sanger sequence assembly in 4 simple steps

Step 1

Input reads and reference sequence (if using) and set automated quality and vector trimming

Step 2

(Optional) Preview chromatograms and manually trim ends

Step 3

Run assembly

Step 4

Analyze assembly, including evaluating coverage and conflicts

Learn more about our Sanger Sequence Assembly Software

Resources | Tutorials | FAQs | Citations | User Guide

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Resources

Please see our resources below for more information on our Sanger sequence assembly tools.

What’s New in SeqMan Ultra 17.2?

Watch Webinar

Get to Know SeqMan Ultra Webinar

Watch Webinar

Transitioning from SeqMan Pro to SeqMan Ultra Webinar

Watch Webinar

Accuracy of de novo assembly of Sanger trace data: SeqMan Pro versus three
alternative pipelines

Read White Paper

Dr. Michael Pauly of Mapp Biopharmaceutical on Ebola and ZMapp

Read Blog Post

Lasergene Molecular Biology Overview

View Document

Tutorials

Watch one of our videos tutorials or check out one of our written tutorials to learn more about our Sanger sequence assembly tools.

Reference Guided Alignment of Sanger/ABI Data

See how to align Sanger/ABI data from multiple samples to a reference sequence or genome. Compare samples, investigate trace and quality data, and analyze SNPs quickly and easily with SeqMan Ultra.

De Novo Assembly and Analysis of Sanger/ABI Data

See how to quickly and easily assemble Sanger/ABI sequencing data and perform downstream analysis. This video shows you how to complete assembly setup, visualization, assembly editing and trimming, and BLAST search using SeqMan Ultra.

Gap Closure After De Novo Assembly Using SeqMan Ultra

Learn how to complete a gap closure after completing a de novo assembly. This video walks you through three different methods you can try based on your specific data.

FAQs

What’s the difference between SeqMan NGen, SeqMan Ultra, and SeqMan Pro?

SeqMan NGen and SeqMan Ultra are two applications that work together to assemble and analyze both Sanger and NGS sequencing data. SeqMan NGen is the application that assembles…

SeqMan NGen and SeqMan Ultra are two applications that work together to assemble and analyze both Sanger and NGS sequencing data. SeqMan NGen is the application that assembles and aligns the data, and is fully integrated in SeqMan Ultra so that you can go from streamlined project setup to finished assembly all in one application. SeqMan Ultra is one of the sequence assembly tools that allows you to analyze and edit the assembly produced by SeqMan NGen. (Additional applications within Lasergene Genomics are available for analyzing NGS projects and more complex Sanger assemblies).

SeqMan Ultra is the new face of SeqMan Pro, our longstanding sequence assembly software application, complete with a new modern, intuitive interface, as well as lots of performance improvements under the hood. SeqMan Ultra is a 64-bit application, which means when compared to the 32-bit SeqMan Pro application, it offers faster project opening, better performance for analyzing large files, increased capacity, and compatibility with macOS 10.15. SeqMan Pro will still be available in Lasergene 17, but will eventually be completely replaced by SeqMan Ultra.

How is the consensus sequence calculated?

SeqMan NGen uses a proprietary “Trace Evidence” algorithm for Sanger sequence assemblies that has significantly better consensus calling accuracy than the “Majority” method used by most consensus calling programs.

How do I get best possible results in my de novo Sanger assembly?

De novo assembly is sensitive to low quality or untrimmed vector sequences. Our sequence assembly tool provides fast and accurate trimming options based on quality and vector (or other contaminant) sequences.

Can your sequence assembly tools assemble multiple samples for variant analysis?

Yes. When you set up your Sanger sequence assembly project in SeqMan NGen, choose “Multi-Sample” when adding your input sequences. You can then groups your reads into experiment groups, making it easy to compare samples in the finished project.

Can I edit a de novo Sanger sequence assembly?

Yes. A de novo assembly run in SeqMan NGen produces a fully editable project file (.sqd) that can be opened in SeqMan Ultra, where base-level and contig-level editing can be carried out.

What file types can I import to assemble?

For Sanger sequence assembly projects, SeqMan NGen accepts output from most Lasergene applications as well as 454, ABI, ALX, FASTA, GCG, GenBank, Phred, SCF, Sequencher, .eff, .fof, .txt and .zip files.

When should I assemble sequences using a reference?

A known sequence can be used as a backbone/template/reference sequence upon which to build your sequence assembly. This lets you perform the assembly with lower average sequence coverage, thus saving a substantial amount of sequencing effort. Simply choose a reference-guided workflow when you set up your project, and you will be prompted to input a reference sequence. If no reference sequence is available for your organism, try using one from a closely-related organism.

Can I add new data to my sequence assembly?

Yes, you can add new sequences to a draft genome assembly in SeqMan Ultra for the purpose of scaffold gap closure. Simply select two adjacent contigs in a scaffold and then choose Contig>Add sequences to close gap to add one or more sequences to close the gap.

How do I organize contigs in my sequence assembly?

There are several options for organizing contigs in an assembly. If your input data is paired, you can use Contig>Order Contigs to automatically create scaffolds based on the paired data. You can also select contigs and use Contig>New Scaffold to manually create scaffolds or simply drag and drop contigs to reposition in the Explorer panel. If you use the Hybrid reference-guided/de novo assembly workflow, contigs will automatically be placed in scaffolds based on the reference positions.

How do I align/join contigs in my Sanger sequence assembly?

Select two or more contigs in the Explorer panel and use Contig>Align contigs end to end to align a multiple contigs to each other. If your contigs are in a scaffold, this alignment will preserve the position within the scaffold and greatly reduce the chance for misaligning contigs at repetitive elements. You can also manually align contigs using Contig>Force Join if you know that two contigs should be merged, but there is insufficient overlap for successful alignment.

What options do I have for editing contigs and contig consensi in my sequence assembly?

SeqMan Ultra offers several options for large scale contig editing, including: splitting (where mismatches occur), reverse complementing, deleting, and micro-editing to remove errors from the consensus. The navigation toolbar allows you to quickly and efficiently search the consensus for conflicts to manually edit.

How can I export my completed sequence assembly?

From SeqMan Ultra, select Contig > Export Consensus and choose from the following options:

Single File – all selected contigs are saved in a single file.
Multiple Files – each selected contig is saved as a separate file.

How can I see my DNA chromatograms?

In SeqMan Ultra, open the Alignment view, then click the plus sign to the left of a sequence name to display its chromatogram. Chromatograms are available only for ABI sequences.

Can I export an image of my Sanger sequence assembly?

Yes, you can easily export an image of your assembly for collaboration or publication in PDF, Bitmap, or PPT format by selecting File>Export Image>Alignment.

Citations

Temporal and Spatial Expression of Arabidopsis Gene Homologs Control Daylength Adaptation and Bulb Formation in Onion (Allium cepa L.)
Rashid, M.H.A., Cheng, W. & Thomas, B. Sci Rep 9, 14629 (2019) doi:10.1038/s41598-019-51262-1.

Screening and Transcriptional Analysis of Polyketide Synthases and Non-ribosomal Peptide Synthetases in Bacterial Strains From Krubera–Voronja Cave
Bukelskis D, Dabkeviciene D, Lukoseviciute L, Bucelis A, Kriaučiūnas I, Lebedeva J and Kuisiene N (2019). Front. Microbiol. 10:2149. doi: 10.3389/fmicb.2019.02149.

Molecular analysis of cox-1 and 18S rRNA gene fragments of Eimeria species isolated from endangered grouse: capercaillie (Tetrao urogallus) and black grouse (Tetrao tetrix)
Stenzel, T., Dziewulska, D., Michalczyk, M. et al. Parasitol Res (2019) 118: 461. https://doi.org/10.1007/s00436-018-6171-5.

Identification and phylogenetic analysis of oral Veillonella species isolated from the saliva of Japanese children
Djais AA, Theodorea CF, Mashima I et al. F1000Research 2019, 8:616.

A novel missense mutation in HSF4 causes autosomal-dominant congenital lamellar cataract in a British family.
Berry, V., Pontikos, N., Moore, A. et al. Eye 32, 806–812 (2018) doi:10.1038/eye.2017.268.

Development of microsatellite markers for Thekopsora areolata, the causal agent of cherry spruce rust
Capador, H, Samils, B, Olson, Å. For Path. 2018; 48:e12413.

Emerging corneal pathogens: First report of Pseudopestalotiopsis theae keratitis
Sayali Sane, Savitri Sharma, Ranjith Konduri, Merle Fernandes. Indian J Ophthalmol. 2019 Jan; 67(1): 150–152. doi: 10.4103/ijo.IJO_791_18.

Influenza D Virus in Cattle, Ireland
Flynn O, Gallagher C, Mooney J, et al. Emerging Infectious Diseases 2018;24(2):389-391. doi:10.3201/eid2402.170759.

Germline variation in O6-methylguanine-DNA methyltransferase (MGMT) as cause of hereditary colorectal cancer
Sami Belhadj, Cátia Moutinho, Pilar Mur, Fernando Setien, Pere Llinàs-Arias, Montserrat Pérez-Salvia, Tirso Pons, Marta Pineda, Joan Brunet, Matilde Navarro, Gabriel Capellá, Manel Esteller, Laura Valle. Cancer Letters, Volume 447, 2019, Pages 86-92, ISSN 0304-3835.

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Just works like it should
“SeqMan has proven to be invaluable to the lab for assembling and editing sequencing projects using capillary sequence data from the ABI 3130 and 3730 sequencing platform. This is one of those applications that just works like it should.”
Kevin Kunstman, Northwestern University Medical School
A great application
“SeqMan Pro is a great application to assemble multiple sequence reads (sequence text or other proprietary format including ABI format) to contigs. Assembled contig can be easily assessed and amended by looking into original data in a single window.”
Shin-ichiro Hiraga, University of Aberdeen
Everything I need in one spot
“I like this program because I can have everything I need in one spot. It is easy to mark a reference sequence to ensure that sequences are align properly when multiple sequences are used and it is just as easy to unmark the reference so as not to influence the consensus sequence. The ability to send consensus to MegAlign and other programs is also especially helpful. I’d say the best part of SeqMan Pro is having the chromatagrams from the sequence reads. It’s incredibly helpful so I can examine the quality of the data that was sent out to me without having to open another program.”
Lauren Kreimer, University of Nebraska-Lincoln
Very reliable and easy to use
“SeqMan Pro is a great application for identifying gene mutations/polymorphisms. It is very reliable and easy to use.”
Sevasti Koukouritaki, Medical College of Wisconsin
Removes the need to manually look for differences
“Quick alignments and easy labels remove the need to manually look for differences. It’s easy to assess confidence in sequencing nucleotides as well.”
Junbum Im, BC Cancer Research Agency

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