minimap2

History

Heng Li 5b10667967 sim-eval.js to support mason2 read names and SAM		2017-08-07 13:28:33 -04:00
..
README.md	renamed simulation-related scripts	2017-08-07 13:26:25 -04:00
mapstat.js	r219: fixed a bug caused by skipping tandem seeds	2017-07-28 14:06:56 -04:00
paf2aln.js	blast-like output working	2017-08-04 14:31:21 -04:00
sam2paf.js	copied sam2paf.js here for completeness	2017-08-04 14:44:37 -04:00
sim-eval.js	sim-eval.js to support mason2 read names and SAM	2017-08-07 13:28:33 -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

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.