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ALLMAPS orders scaffolds by maximizing colinearity to a collection of genetic/genomic maps into the final chromosome build.

NOTE: This is step two: using the merged maps and weight files to generate the map.

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. We highlight several salient features of ALLMAPS.

  • 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

Quick Start

Test Data

Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> ALLMAPS-testdata.

Input File(s)


  • JM-2.bed
  • scaffolds.fasta
  • weights.txt

from the directory above as test input.

Parameters Used in App

  • No Parameters are used

Output File(s)

Can be viewed in the example data directory: /iplant/home/shared/iplantcollaborative/example_data/ALLMAPS-testdata/Example_output_PATH

Tool Source for App