De Novo Genome Assembly

Use Lasergene Genomics for easy and accurate de novo genome assembly.

De novo genome assembly can be a very difficult computational problem and often presents issues of speed and accuracy due to the large volume of sequences, the presence of repeated regions, and the significant amount of RAM required. Lasergene Genomics makes it easy to perform a de novo assembly by guiding you through various approaches to meet your needs. In addition to the traditional de novo workflow, often most useful with mate pair or paired-end data, Lasergene Genomics also offers a hybrid approach, which aligns sequences to a closely related reference genome, identifies variations (SNPs, deletions, and insertions) and automatically resolves the insertions via de novo assembly. A genome polishing workflow is also available that uses Illumina data to improve the accuracy of Canu or Spades draft genome assemblies of PacBio and Oxford Nanopore long read data. Whatever your approach, Lasergene Genomics creates the most accurate, complete assemblies possible and provides you with detailed statistics for each fully-editable assembly, as well as excellent visualization and post-assembly analysis tools.

De novo genome assembly in 4 simple steps

Step 1

Specify sequences and parameters for assembly

Step 2

Check for conflicts and evaluate coverage

Step 3

Group assembled contigs into scaffolds

Step 4

Add sequences to close gaps

Learn more about De Novo Genome Assembly

Resources | Tutorials | FAQs | Citations | User Guide

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Resources

Please see our resources below for more information on de novo genome assembly.

Genome Polishing Benchmarks: SeqMan NGen vs. Three Open-Source Tools

Read White Paper

Cloud Assemblies for NGS Sequences

Watch Webinar

Microbial Genome Assembly and Analysis Webinar

Watch Webinar

Decreased Memory Requirements for De Novo Genome Assembly

Read Blog Post

Tutorials

Watch one of our videos or check out one of our written tutorials to learn more about using Lasergene Genomics for de novo genome assembly.

Merging Contigs After an Assembly Using SeqMan Pro

In this video, we show you how to merge contigs in SeqMan Pro following a de novo genome assembly or a templated assembly where contigs have been split based on detected structural variations.

Editing the Alignment in SeqMan Pro

In this video, we’ll look at the editing options available in SeqMan Pro for *.sqd project files, including trimming and un-trimming individual sequences and groups of sequences, removing conflicts or gaps from the consensus, direct editing of aligned sequences, alignment adjustments, and exporting the edited consensus and aligned reads.

Annotating the Consensus

Learn about the four primary ways to annotate your consensus sequence following an assembly.

FAQs

What sequence technologies do you support for de novo genome assembly?

When performing de novo genome assembly, SeqMan NGen supports Illumina, Oxford nanopore, Sanger/ABI and Ion Torrent sequencing technologies.

How can a reference genome be used to improve a de novo assembly?

In SeqMan NGen’s “Hybrid reference guided/de novo assembly” workflow, the reference sequence for a related microbial strain is used to guide the initial assembly. Novel regions are assembled de novo, automatically producing a genome scaffold of the sequence strain.

Do your de novo assembly tools support the assembly of large genomes?

If you have a DNASTAR Cloud Assembly license, you can de novo assemble even the largest of genomes on the cloud using any inexpensive Windows or Macintosh laptop. If you are performing the assembly on a local computer, rather than the cloud, the answer depends on the computer’s available memory. Here are examples of the committed RAM necessary to de novo assemble different organisms at 50x coverage: E. coli = 12 GB, S. cervisiae = 17 GB, N. crassa = 28 GB, C. elegans = 61 GB.

Can I edit assembly projects and close genomes?

Yes, our de novo assembly software, SeqMan NGen, outputs fully-editable project files in .sqd format that can be edited in SeqMan Ultra. Both sequences and contigs can be edited and contigs can be organized into genome scaffolds to facilitate genome closure editing.

Does Lasergene Genomics support assembly using long read technologies?

We offer a workflow to polish or improve existing Canu or Spades assemblies of Oxford Nanopore Technologies and PacBio long read data with Illumina data, producing a highly accurate assembly in an editable SeqMan Ultra project file.

We are also currently developing new workflows for assembly of Oxford Nanopore Technologies and PacBio sequencing data. This functionality is expected to be available in 2020.

Citations

Genome Sequences of 12 Pseudomonas lundensis Strains Isolated from the Lungs of Humans
Brittan S. Scales, John R. Erb-Downward, Nicole R. Falkowski, John J. LiPuma, Gary B. Huffnagle. Genome Announcements Feb 2018, 6 (7) e01461-17; DOI: 10.1128/genomeA.01461-17.

Clonal diversity and spatial genetic structure in the long-lived herb, Prairie trillium
Mandel, Jennifer R et al. PloS one vol. 14,10 e0224123. 21 Oct. 2019, doi:10.1371/journal.pone.0224123.

Development and Validation of a Reference Data Set for Assigning Staphylococcus Species Based on Next-Generation Sequencing of the 16S-23S rRNA Region
Kosecka-Strojek M, Sabat AJ, Akkerboom V, Becker K, van Zanten E, Wisselink G, Miedzobrodzki J, Kooistra-Smid AMD and Friedrich AW (2019). Front. Cell. Infect. Microbiol. 9:278. doi: 10.3389/fcimb.2019.00278.

Molecular investigation of isolates from a multistate polymicrobial outbreak associated with contaminated total parenteral nutrition in Brazil
Pillonetto, M., Arend, L., Gomes, S.M.T. et al. BMC Infect Dis 18, 397 (2018) doi:10.1186/s12879-018-3287-2.

Draft Genome Sequence of Anoxybacillus sp. Strain UARK-01, a New Thermophilic Lignin-Utilizing Bacterium Isolated from Soil in Arkansas, USA
Thamir H. Alkahem Albalawi, Douglas D. Rhoads, Ravi D. Barabote. Genome Announcements Jul 2017, 5 (30) e00588-17; DOI: 10.1128/genomeA.00588-17.

PVL overexpression due to genomic rearrangements and mutations in the S. aureus reference strain ATCC25923
Stieber, B., Sabat, A., Monecke, S. et al. BMC Res Notes 10, 576 (2017) doi:10.1186/s13104-017-2891-3.

Complete genome sequences of two strains of Treponema pallidum subsp. pertenue from Ghana, Africa: Identical genome sequences in samples isolated more than 7 years apart
Strouhal M, Mikalová L, Havlíčková P, Tenti P, Čejková D, et al. (2017) PLOS Neglected Tropical Diseases 11(9): e0005894.

Characterization and Recognition of Brachyspira hampsonii sp. nov., a Novel Intestinal Spirochete That Is Pathogenic to Pigs
Nandita S. Mirajkar, Nyree D. Phillips, Tom La, David J. Hampson, Connie J. Gebhart. Journal of Clinical Microbiology Nov 2016, 54 (12) 2942-2949; DOI: 10.1128/JCM.01717-16.

Draft Genome Sequences of Seven Pseudomonas fluorescens Subclade III Strains Isolated from Cystic Fibrosis Patients
Brittan S. Scales, John R. Erb-Downward, Ian M. Huffnagle, John J. LiPuma, Gary B. Huffnagle. Genome Announcements Jan 2015, 3 (1) e01285-14; DOI: 10.1128/genomeA.01285-14

Novel Temperate Phages of Salmonella enterica subsp. salamae and subsp. diarizonae and Their Activity against Pathogenic S. enterica subsp. enterica Isolates
Mikalová L, Bosák J, Hříbková H, Dědičová D, Benada O, et al. (2017) PLOS ONE 12(1): e0170734.

Characterization of Tn3000, a Transposon Responsible for blaNDM-1 Dissemination among Enterobacteriaceae in Brazil, Nepal, Morocco, and India
Juliana Coutinho Campos, Maria José Félix da Silva, Paulo Roberto Nascimento dos Santos, Elaine Menezes Barros, Mayne de Oliveira Pereira, Bruna Mara Silva Seco, Cibele Massotti Magagnin, Leonardo Kalab Leiroz, Théo Gremen Mimary de Oliveira, Célio de Faria-Júnior, Louise Teixeira Cerdeira, Afonso Luís Barth, Suely Carlos Ferreira Sampaio, Alexandre Prehn Zavascki, Laurent Poirel, Jorge Luiz Mello Sampaio. Antimicrobial Agents and Chemotherapy Nov 2015, 59 (12) 7387-7395; DOI: 10.1128/AAC.01458-15.

Complete package
“This is the complete package, from assembly to analysis”
Marjorie Beggs, Arkana Laboratories
I recommended it highly
“I have never experienced a problem with this easy to use package…I recommended it highly.”
Dr. Andrew M. Kropinski, University of Guelph
Versatile
“Versatile for bacterial and vertebrate genomes.”
Douglas Duane Rhoads, University of Arkansas Biological Sciences Dept

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