Align the reads

First, we’ll use minimap2 to align the sequencing paired-end reads in reads_R1.fq and reads_R2.fq to the reference genome located at $REF. Run the following:

Let’s make some sense of this minimap2 command:

• -a tells minimap2 that we want it to output the results in the SAM format
• -o reads.mapped.sam tells minimap2 that we want to write the output SAM results to the file reads.mapped.sam (rather than printing them to standard output)
• -x sr tells minimap2 that we want to use its short-read mapping preset
  • This is because our reads were sequenced using an Illumina short-read sequencer
• Next, we’re specifying the reference genome: $REF_FASTA
• Lastly, we’re specifying the read files we want to map: reads_R1.fq and reads_R2.fq

After running the above command, we will have successfully mapped our reads (reads_R1.fq and reads_R2.fq) to the reference genome ($REF) and written the results to the file reads.mapped.sam.

To see the first few lines of the SAM output file in the human-readable SAM format, run the following:

The first few lines (beginning with @) are SAM header lines, and the rest of the lines are SAM alignments, one line per read or mate. See the SAM specification for details about how to interpret the SAM file format.