nf-core/bamtofastq

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Introduction nf-core/bamtofastq is a bioinformatics best-practice analysis pipeline that converts (un)mapped .bam or .cram files into fq.gz files. Initially, it auto-detects, whether the input file contains single-end or paired-end reads. Following this step, the reads are sorted using samtools collate and extracted with samtools fastq. Furthermore, for mapped bam/cram files it is possible to only convert reads mapping to a specific region or chromosome. The obtained FastQ files can then be used...