[minimap2 v2.8] (https://github.com/lh3/minimap2/releases/tag/v2.8)
This app runs minimap2 to align Oxford Nanopore reads in a fastq file to a reference sequence.
This app should be used aligning Oxford Nanopore reads to a reference sequence
The app requires a FASTQ file containing Oxford Nanopore reads and a reference FASTA to align to.
The app outputs 2 files:
- sorted BAM file
- BAM index file
The app runs minimap2 using the Oxford Nanopore settings to output a SAM file. It then uses samtools v1.5 (docker image: [quay.io/biocontainers/samtools:1.5--2] (https://quay.io/repository/biocontainers/samtools?tab=info)) to convert SAM to BAM, sort and index.
This app should only be used for Oxford Nanopore data.