DNASTAR

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 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?

Yes. Lasergene 17.1 offers three beta workflows for long read data from Oxford Nanopore and PacBio:

1. De novo assembly of long read sequencing data, with optional read correction.
2. De novo assembly of long read sequencing data, followed by short read polishing and assembly correction.
3. 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.