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added paf2aln.js example

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Heng Li 2017-08-04 14:51:33 -04:00
parent 269b8661b9
commit b40598fa91
1 changed files with 4 additions and 1 deletions
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misc/README.md
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@ -4,7 +4,10 @@ page][k8].
* [paf2aln.js](paf2aln.js): convert PAF to [MAF][maf] or BLAST-like output for * [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 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 * [mapstat.js](mapstat.js): output basic statistics such as the number of
non-redundant mapped bases, number of split and secondary alignments and non-redundant mapped bases, number of split and secondary alignments and