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Difference between revisions of "SW:AAF"

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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 ]]

Revision as of 11:50, 4 August 2020

AAF

GCATemplates available: ada

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