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Difference between revisions of "SW:AAF"

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== AAF ==
 
== AAF ==
[[SW:GCATemplates|GCATemplates]] available: [https://github.tamu.edu/cmdickens/GCATemplates/blob/master/templates/ada/run_aaf_20160518_ada.sh ada]
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[[SW:GCATemplates|GCATemplates]] available: [https://github.tamu.edu/cmdickens/GCATemplates/blob/master/templates/grace/run_aaf_20171001_grace.sh grace]
  
 
AAF [https://sourceforge.net/projects/aaf-phylogeny/ homepage]
 
AAF [https://sourceforge.net/projects/aaf-phylogeny/ homepage]
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It takes raw sequencing reads from each sample altogether and generates a distance matrix based on the proportion of shared k-mers between each sample and reconstruct a phylogeny based on the distance matrix.
 
It takes raw sequencing reads from each sample altogether and generates a distance matrix based on the proportion of shared k-mers between each sample and reconstruct a phylogeny based on the distance matrix.
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If you are running aaf_distance.py with > 10 cores and the command is failing with a message like '''''IndexError: list index out of range''''' then use fewer cores such as -t 5
  
 
[[ Category:SW ]] [[ Category: Bioinformatics ]]
 
[[ Category:SW ]] [[ Category: Bioinformatics ]]

Latest revision as of 10:52, 8 July 2021

AAF

GCATemplates available: grace

AAF homepage

Use the module spider command to see the available versions of AAF:

 module spider AAF

AAF (alignment and assembly-free) is a free software package that reconstructs phylogeny from next-generation sequencing data without assembly and alignment.

It takes raw sequencing reads from each sample altogether and generates a distance matrix based on the proportion of shared k-mers between each sample and reconstruct a phylogeny based on the distance matrix.

If you are running aaf_distance.py with > 10 cores and the command is failing with a message like IndexError: list index out of range then use fewer cores such as -t 5