diff --git a/misc/README.md b/misc/README.md index b50cac9..1a100fe 100644 --- a/misc/README.md +++ b/misc/README.md @@ -4,7 +4,10 @@ page][k8]. * [paf2aln.js](paf2aln.js): convert PAF to [MAF][maf] or BLAST-like output for eyeballing. PAF has to be generated with minimap2 option `-S`, which writes - the aligned sequences to the `cs` tag. + the aligned sequences to the `cs` tag. An example: + ```sh + ../minimap2 -S ../test/MT-*.fa | k8 paf2aln.js /dev/stdin + ``` * [mapstat.js](mapstat.js): output basic statistics such as the number of non-redundant mapped bases, number of split and secondary alignments and