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cnobles / iGUIDE

Bioinformatic pipeline for identifying dsDNA breaks by marker based incorporation, such as breaks induced by designer nucleases like Cas9.
https://iguide.readthedocs.io/en/latest/
GNU General Public License v3.0
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Implement system for alternative aligners #54

Closed cnobles closed 5 years ago

cnobles commented 5 years ago

Implement system in config to allow for alternative aligners with a SAM/BAM standardized output. This will likely require the user to know a little about snakemake as they would need to write the 'run' statement in the correct format, example could be provided with bwa.

Additionally, an analysis script would need to be put together that will output the same / similar file types to that of couple.R (uniq.csv, multihit.rds, chimeras.rds). This script would need to be written following the practices of the Bushman lab.

cnobles commented 5 years ago

In #60, implemented a system for BWA to be used as an aligner and laid ground work for additional SAM/BAM-output aligners to be developed for iGUIDE.