28 lines
1.2 KiB
Markdown
28 lines
1.2 KiB
Markdown
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The [K8 Javascript engine][k8] is needed to run Javascripts in this directory.
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Precompiled k8 binaries for Mac and Linux can be found at the [K8 release
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page][k8].
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* [paf2aln.js](paf2aln.js): convert PAF to [MAF][maf] or BLAST-like output for
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eyeballing. PAF has to be generated with minimap2 option `-S`.
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* [mapstat.js](mapstat.js): output basic statistics such as the number of
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non-redundant mapped bases, number of split and secondary alignments and
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number of long gaps. This scripts seamlessly works with both SAM and PAF.
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* [pbsim2fa.js](pbsim2fa.js): convert reads simulated with [PBSIM][pbsim] to
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FASTA and encode the true mapping positions to read names.
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* [pbsim-eval.js](pbsim-eval.js): evaluate mapping accuracy for FASTA generated
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with [pbsim2fa.js](pbsim2fa.js). This script only works with PAF. For SAM,
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please run the following instead:
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```sh
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k8 sam2paf.js -p aln.sam | k8 pbsim-eval.js /dev/stdin
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```
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* [sam2paf.js](sam2paf.js): convert SAM to PAF.
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[k8]: https://github.com/attractivechaos/k8
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[k8bin]: https://github.com/attractivechaos/k8/releases
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[maf]: https://genome.ucsc.edu/FAQ/FAQformat#format5
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[pbsim]: https://github.com/pfaucon/PBSIM-PacBio-Simulator
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