The ordering and orientation of genomic scaffolds to reconstruct chromosomes is an essential step during de novo genome assembly. This process is often assisted by various mapping techniques. Because each map provides a unique line of evidence, a combination of multiple maps can greatly improve the accuracy of the resulting chromosomal assemblies. ALLMAPS is capable of computing a scaffold ordering that maximizes the colinearity to a collection of maps, including genetic, physical or comparative maps into the final chromosome build. The major features are:

  • Clear, computable objective which is to maximize the colinearity to multiple input maps - reproducible
  • Allow variable weights in input maps, leading to better control in conflict resolution - flexible
  • Can incorporate many mapping evidence, requiring minimal transformation - powerful
  • Streamline the genome build (with FASTA and AGP outputs) and genome update (with CHAIN output) - easy-to-use

Accessing the software

To load the module:

$ module load ALLMAPS/0.8.4-iomkl-2018a-Python-2.7.14

An example command to include in your job script:

python -m jcvi.assembly.allmaps path JM-2.bed scaffolds.fasta -w weights.txt

Accessing Previous Versions

Wherever possible, previous versions of this application will be retained for continuity, especially for research projects that require a consistent version of the software throughout the project. Such versions, however, may be unsupported by IT Services or the applications vendor, and may be withdrawn at short or no notice if they can no longer run on the cluster - for example, essential operating system upgrades may be incompatible with old versions.

At present there are no previous versions of this application on the BlueBEAR service.

Known Problems & Limitations


Other Information

The Support Level for this application is An.

Visit the ALLMAPS Github repository for more information regarding this application.

Last modified: 20 June 2018