29 lines
1.3 KiB
Markdown
29 lines
1.3 KiB
Markdown
The [K8 Javascript shell][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][k8bin].
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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`, which writes
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the aligned sequences to the `cs` tag. An example:
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```sh
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../minimap2 -S ../test/MT-*.fa | k8 paf2aln.js /dev/stdin
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```
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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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* [sim-pbsim.js](sim-pbsim.js): convert reads simulated with [PBSIM][pbsim] to
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FASTA and encode the true mapping positions to read names in a format like
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`S1_33!chr1!225258409!225267761!-`.
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* [sim-eval.js](sim-eval.js): evaluate mapping accuracy for FASTA generated
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with [sim-pbsim.js](sim-pbsim.js) or [sim-mason2.js](sim-mason2.js).
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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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