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minimap2/misc/README.md

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The K8 Javascript shell is needed to run Javascripts in this directory. Precompiled k8 binaries for Mac and Linux can be found at the K8 release page.

  • paf2aln.js: convert PAF to 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. An example:

    ../minimap2 -S ../test/MT-*.fa | k8 paf2aln.js /dev/stdin

  • mapstat.js: output basic statistics such as the number of non-redundant mapped bases, number of split and secondary alignments and number of long gaps. This scripts seamlessly works with both SAM and PAF.

  • sim-pbsim.js: convert reads simulated with PBSIM to FASTA and encode the true mapping positions to read names in a format like S1_33!chr1!225258409!225267761!-.

  • sim-eval.js: evaluate mapping accuracy for FASTA generated with sim-pbsim.js or sim-mason2.js.

  • sam2paf.js: convert SAM to PAF.