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ALLMAPS

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This workflow links together the two stages of the ALLMAPS pipeline: ALLMAPS merge; ALLMAPS path

ALLMAPS orders scaffolds by maximizing colinearity to a collection of genetic/genomic maps into the final chromosome build. More info: http://goo.gl/KI61Ow

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

Demo data download: https://dl.dropboxusercontent.com/u/15937715/Data/ALLMAPS/ALLMAPS-testdata.zip
Resources: https://github.com/tanghaibao/jcvi/wiki/ALLMAPS
Command line:
- Step 1: python -m jcvi.assembly.allmaps merge JMMale.csv JMFemale.csv -o JM-2.bed -w weights.txt
- Step 2: python -m jcvi.assembly.allmaps path JM-2.bed scaffolds.fasta -w weights.txt

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)

Use

One or more map files (can be genetic maps, genomic maps, etc):
- Example data are JMMale.csv JMFemale.csv
- Format for map data: https://github.com/tanghaibao/jcvi/wiki/ALLMAPS#step-1-prepare-input-data

Parameters Used in App

No Parameters are used in this workflow.

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

https://github.com/tanghaibao/jcvi/wiki/ALLMAPS