• Product manuals

Browse the manual

• Introduction
  • The concept of Long Read Support
  • Contact information
  • System requirements
• Template workflows
  • De Novo Assemble Long Reads and Polish with Short Reads
• Import Nanopore Reads
• De Novo Assemble Long Reads
  • De novo assembly parameters
  • De novo assembly output
• Map Long Reads to Reference
  • Map Long Reads to Reference output
• Polish with Reads
  • Polish with Reads output
• Correct Long Reads
  • Correct Long Reads output
• RNA-Seq Analysis for Long Reads
  • Reads and reference settings
  • Mapping settings
  • Expression settings
  • RNA-Seq Analysis for Long Reads output
• Structural Variant Caller for Long Reads
  • Structural Variant Caller settings
  • Structural Variant Caller output
  • Structural Variant Caller algorithm
• Install and uninstall plugins
  • Installation of plugins
  • Uninstalling plugins
• Bibliography

Bibliography

Cheng et al., 2021

Cheng, H., Concepcion, G., Feng, X., Zhang, H., and H., L. (2021).
Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm.
Nat Methods, 18(2):170-175.

Li, 2018

Li, H. (2018).
Minimap2: pairwise alignment for nucleotide sequences.
Bioinformatics, 34(18):3094-3100.

Mortazavi et al., 2008

Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L., and Wold, B. (2008).
Mapping and quantifying mammalian transcriptomes by rna-seq.
Nat Methods, 5(7):621-628.

Vaser and Šikic, 2021

Vaser, R. and Šikic, M. (2021).
Time-and memory-efficient genome assembly with raven.
Nature Computational Science, 1(5):332-336.

Vaser et al., 2017

Vaser, R., Sovic, I., Nagarajan, N., and Šikic, M. (2017).
Fast and accurate de novo genome assembly from long uncorrected reads.
Genome Research, 27(5):737-746.

Wick and Holt, 2019

Wick, R. R. and Holt, K. E. (2019).
Benchmarking of long-read assemblers for prokaryote whole genome sequencing.
F1000Research, 8:2138.

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