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genomic-medicine-sweden / meta-val

nf-core/taxprofiler post-processing; verification of classification results; consensus maps
MIT License
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Prepare fastq file of mapped reads for each pathogen after mapping against pathogen genomes #23

Open LilyAnderssonLee opened 4 months ago

LilyAnderssonLee commented 4 months ago

Description of feature

The BAM file with mapped reads from the pathogen screening step contains all pathogens. We need to prepare a separate FASTQ file for each pathogen.