Assemblytics

Analyze your assembly by comparing it to a reference genome

Instructions

Upload a delta file to analyze alignments of an assembly to another assembly or a reference genome

  1. Download and install MUMmer
  2. Align your assembly to a reference genome using nucmer (from MUMmer package)

    $ nucmer -maxmatch -l 100 -c 500 REFERENCE.fa ASSEMBLY.fa -prefix OUT

    Consult the MUMmer manual if you encounter problems

  3. Optional: Gzip the delta file to speed up upload (usually 2-4X faster)

    $ gzip OUT.delta
    Then use the OUT.delta.gz file for upload.

  4. Upload the .delta or delta.gz file (view example) to Assemblytics
Important: Use only contigs rather than scaffolds from the assembly. This will prevent false positives when the number of Ns in the scaffolded sequence does not match perfectly to the distance in the reference.

Run Assemblytics

Description

Unique sequence length required

Minimum variant size