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Heng Li 269b8661b9 minor clarification 2017-08-04 14:49:25 -04:00
..
README.md minor clarification 2017-08-04 14:49:25 -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
pbsim-eval.js minor tweaks to the evaluation script 2017-08-01 13:52:29 -04:00
pbsim2fa.js convert pbsim .maf to fasta 2017-07-25 13:54:58 -04:00
sam2paf.js copied sam2paf.js here for completeness 2017-08-04 14:44:37 -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.

  • 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.

  • pbsim2fa.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!-.

  • pbsim-eval.js: evaluate mapping accuracy for FASTA generated with pbsim2fa.js. This script only works with PAF. For SAM, please convert to PAF first:

    k8 sam2paf.js -p aln.sam | k8 pbsim-eval.js /dev/stdin

  • sam2paf.js: convert SAM to PAF.