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  3. Alignment and Assembly

Alignment and Assembly

  • Best practice for preprocessing NGS reads in Geneious Prime
  • How do I assemble F and R pairs of Sanger sequences?
  • Assembly of SARS-CoV-2 genomes from tiled amplicon Illumina sequencing using Geneious Prime
  • What are the hardware requirements for assembly of NGS data using the Geneious de novo Assembler?
  • Can Geneious Prime assemble PacBio or Minion data?
  • Can I perform a hybrid assembly with Illumina and PacBio/MinION data?
  • How do I set up Windows 10/11 to run SPAdes, Flye, or STAR assemblers?
  • Which multiple alignment algorithm should I use?
  • How do I delete all gaps in my alignment?
  • Can I call SNPs on individual sequences aligned to a reference?
  • How do I map peptides to a protein sequence?
  • What’s the difference between Pairwise/Multiple alignment, de novo Assembly, and Map to Reference?
  • Which de novo assembly algorithm is best for my data?
  • Which map to reference assembly algorithm is best for my data?
  • How do I strip alignment columns in R10 and above?
  • Where can I get reference databases for chimera filtering?
  • How do I assemble paired reads?
  • Can the Geneious assembler do scaffolding?
  • How do I use the advanced assembly settings?
  • Can I use multiple reference sequences in my assembly?
  • What’s the difference between soft trimming and hard trimming in Geneious Prime?
  • Why is my alignment taking so long?
  • Error: Your operating system won't allow Geneious to open enough files simultaneously to perform the operation
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