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lines changed- public/examples/viralrecon
- assembly
- cutadapt
- fastqc
- log
- fastp
- fastqc
- raw
- trim
- kraken2
- pipeline_info
- variants
- bowtie2
- log
- mosdepth
- amplicon
- genome
- picard_metrics
- samtools_stats
- ivar
- asciigenome
- SAMPLE1_PE
- SAMPLE2_PE
- SAMPLE3_SE
- bcftools_stats
- consensus/bcftools
- base_qc
- nextclade
- pangolin
- quast
- aligned_stats
- basic_stats
- contigs_reports
- minimap_output
- genome_stats
- icarus_viewers
- log
- snpeff
- bcftools_stats
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