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Have you thought about using minimap2? It has a Python API (mappy) which you could use to iterate over a fastq file and quickly identify reads which map to one of the potential contaminant genomes.
Hello, friend! Could you show the changes that were made in config.yaml. I am trying to decontaminate a tryp genome, but I get lost in this procedure. Thx!
Have you thought about using minimap2? It has a Python API (mappy) which you could use to iterate over a fastq file and quickly identify reads which map to one of the potential contaminant genomes.
ReplyDeletethanks for the information. I have not used minimap2 yet, fastq_screen seems to be doing OK for me.
DeleteHello, friend! Could you show the changes that were made in config.yaml. I am trying to decontaminate a tryp genome, but I get lost in this procedure. Thx!
ReplyDelete