Lasergene Genomics simplifies de novo genome assembly for projects without a reference sequence. Powered by SeqMan NGen, automated workflows make it easy to generate accurate, high-quality assemblies with speed and efficiency, even on modestly equipped computers.
Key Features
Specify sequences and parameters for assembly
Check for conflicts and evaluate coverage
Group assembled contigs into scaffolds
Add sequences to close gaps
Please see the resources below for more information on our de novo genome assembly software.
Using Lasergene to De Novo Assemble PacBio HiFi Data
How to Assemble Genomes like a Bioinformatics Pro
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.
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.
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.
De novo assembly is a method for constructing genomes from a large number of DNA fragments, with no prior knowledge of the correct sequence or order of those fragments. The process involves the assembly of DNA fragments, or reads, into overlapping oriented contigs, which are then joined into scaffolds and eventually a single chromosome with the help of de novo assembly tools.
When performing de novo genome assembly, SeqMan NGen supports Illumina, Oxford Nanopore, PacBio, Sanger/ABI, and Ion Torrent sequencing technologies.
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.
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.
Yes, our genome 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.
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:
All three workflows produce a highly accurate assembly in an editable SeqMan Ultra project file.
| 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 |
The complete genome sequence of unculturable Mycoplasma faucium obtained through clinical metagenomic next-generation sequencing. Sabat AJ, Durfee T, Baldwin S, et al. (2024). Front. Cell. Infect. Microbiol., 15 April 2024. https://doi.org/10.3389/fcimb.2024.1368923
Whole-genome sequencing and genetic characteristics of representative porcine reproductive and respiratory syndrome virus (PRRSV) isolates in Korea
Kim, SC., Moon, SH., Jeong, CG. et al. (2022). Virol J 19, 66. https://doi.org/10.1186/s12985-022-01790-6.
De novo cloning and functional characterization of a mechanosensitive piezo-like ion channel in the crayfish
Ergin B, Saglam B, Arslan K, Coskun Beyatli N, Taskiran ZE, Bastug T, Purali N. (2023). Cell Physiol Biochem. Jul 29;57(4):226-237. https://doi.org/10.33594/000000640. PMID: 37515574.
Structural and functional insights into the ATP-binding cassette transporter family in the corn planthopper, Peregrinus maidis
Wang, Y.-H., Klobasa, W., Chu, F.-C., Huot, O., Whitfield, A.E. & Lorenzen, M. (2023). Insect Molecular Biology, 32(4), 412–423. https://doi.org/10.1111/imb.12840.
Differential viral genome diversity of healthy and RSS-affected broiler flocks
Kubacki J, Qi W, Fraefel C. (2022). Microorganisms. 10(6):1092. https://doi.org/10.3390/microorganisms10061092.
Transcriptome software results show significant variation among different commercial pipelines
Thawng, C.N., Smith, G.B. (2023). BMC Genomics 24, 662. https://doi.org/10.1186/s12864-023-09683-w.
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. (2019). 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. (2018). BMC Infect Dis 18, 397. doi:10.1186/s12879-018-3287-2.
