de novo population genomics analysis
de novo population genomics analysis
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a program to perform population genomics analysis of samples for which there is no reference genome. Samples can be in FASTQ or FASTA format. Fst, Fis, ? and expected/observed heterzygosity will be calculated.
Quick Start
- To use de novo population genomics analysis, import your data in fasta or fastq format.
- Resources: http://creskolab.uoregon.edu/stacks/comp/denovo_map.php
Test Data
Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> stacks -> stacks_demo -> de_novo_population_genomics
Input File(s)
Use indv_1.fa up to 20 at the samples for analysis box and the _Community Data -> iplantcollaborative -> example_data -> stacks_demo->_MAP.txt for the population map field
Parameters Used in App
When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below.
- Default parameters only, no further configuration needed.
Output File(s)
Expect several files as an output. For details on what each output means please refer to the manual of the developer of stacks at http://creskolab.uoregon.edu/stacks/manual/