minimap2

History

Heng Li 3a375d3436 renamed paf2ovlp to ov-eval		2017-12-24 18:04:00 -05:00
..
README.md	renamed simulation-related scripts	2017-08-07 13:26:25 -04:00
intron-eval.js	when there are incorrect anno, warn but not abort	2017-11-24 12:48:49 -05:00
mapstat.js	backup manuscript	2017-08-24 22:05:14 +08:00
ov-eval.js	renamed paf2ovlp to ov-eval	2017-12-24 18:04:00 -05:00
paf2aln.js	convert PAF to LAST's cigar output	2017-11-18 20:30:44 -05:00
paf2diff.js	fixed incorrect var coordinate	2017-11-12 20:25:33 -05:00
sam2paf.js	added the /1 or /2 suffix	2017-09-26 12:04:35 -04:00
sim-eval.js	eval script works with /[12] in SAM	2017-09-27 23:33:59 -04:00
sim-mason2.js	sim-eval.js to support mason2 read names and SAM	2017-08-07 13:28:33 -04:00
sim-pbsim.js	sim-eval.js to support mason2 read names and SAM	2017-08-07 13:28:33 -04:00
splice2bed.js	support both SAM and PAF as input	2017-12-02 21:57:19 -05:00

README.md

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.