nxf-minimapper

Nextflow pipeline to map long reads to a reference. Mainly for use in plasmid or amplicon verification. The pipeline accepts a reference file containing one record and either:

• a fastq file or
• a directory of fastq files

It is assumed that each sequence file cotains the reads from one sample that are to be mapped to the reference. It performs alignment of the reads to the reference using minimap2, and generates an Integrated Genomic Viewer html report. The resulting alignments (bam files) can be also visualized in standalone IGV or other software.
Supported reference file formats:

• fasta
• genbank
• EMBL
• Snapgene

Running the pipeline

Only nextflow and docker are needed. The pipeline can be run from the command line

nextflow run angelovangel/nxf-minimapper --ref reference.dna --format snapgene --fastq sample1.fastq

The pipeline can also be imported in EPI2ME and run there. For this, install EPI2ME and import the pipeline using this link:
https://github.com/angelovangel/nxf-minimapper

Output

Results are saved in a folder named output. A bam file is generated for every sample (in output/00-alignments) that can be opened in IGV. To open the alignments in IGV:

• install IGV for your platform (https://igv.org/doc/desktop/#DownloadPage/)
• open reference file - Genomes - Load genome from File - select the reference.fasta file from output/00-alignments
• open alignment - File - Load from File - select one or more bam files

Also, an alignment summary table and IGV report html files are generated, as well as the consensus of the alignment. If you use EPI2ME, all the reports are visible directly there under Reports.