De Novo Genome Assembly

DE NOVO GENOME ASSEMBLY

Easily and accurately perform de novo genome assemblies of Sanger or NGS data, or polish long read assemblies.

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 several genome finishing workflows, for error correction and refinement of draft genomes. We also offer several workflows (currently in beta) for de novo assembly and polishing of long read sequencing data from Oxford Nanopore and PacBio, including PacBio Hifi reads. 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

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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

Choosing the Best Assembly Strategy for Your Genomic Sequencing Data

Watch Webinar

How to Assemble Genomes like a Bioinformatics Pro

Read Blog Post

Cloud Assemblies for NGS Sequences

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.

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 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 “Combined 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 bacterial, fungal, and other small eukaryotic genomes on the cloud using any inexpensive Windows or Macintosh laptop….

If you have a DNASTAR Cloud Assembly license, you can de novo assemble bacterial, fungal, and other small eukaryotic 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 de novo assembly using long read technologies?

Yes. Lasergene 17 offers three beta workflows for de novo assembly of long read data from Oxford Nanopore and PacBio, including PacBio Hifi data:…

Yes. Lasergene 17 offers three beta workflows for de novo assembly of long read data from Oxford Nanopore and PacBio, including PacBio Hifi data:

De novo assembly of long read sequencing data, with optional read correction.
De novo assembly of long read sequencing data, followed by short read polishing and assembly correction.
NGS polishing to improve an existing draft genome assembly (including assemblies from Canu or Spades) with Illumina data.

All three workflows produce a highly accurate assembly in an editable SeqMan Ultra project file.

Benchmarks

*Lasergene Genomics De Novo* Genome Assembly Benchmarks**
	Genome Length (Mbases)	Illumina Read Length	Coverage	ContigN50 (kb)	Largest Contig (bp)	Assembly Time	Data Source
Microbial Genomes
E.coli K12MG1655	4.7	301	100X	155	360,028	1 hr 6 min	Illumina Basespace
Saccharomyces cerevisiae	12	251	100X	59	272,990	5 hr 32 min	ERX1598831
Salmonella enterica	4.7	251	100X	110	310,809	0 hr 39 min	SRA SRX1250164
Eukaryotic Genomes
Aspergillus tubingensis	35	251	80X	215	838,152	6 hr 40 min	ERR1823584
Caenorhabditis elegans	97	251	80X	35	325,695	21hr 8min	DRR142763
Arabidopsis thaliana	120	301	70X	77	1,056,792	17hr 57min	SRR7785174

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.

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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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