zzh
/
minimap2
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

minor clarification

This commit is contained in:
Heng Li 2017-08-04 14:49:25 -04:00
parent 890d7bbd5b
commit 269b8661b9
1 changed files with 6 additions and 4 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

10
misc/README.md
View File

@ -1,20 +1,22 @@
The [K8 Javascript engine][k8] is needed to run Javascripts in this directory. The [K8 Javascript shell][k8] is needed to run Javascripts in this directory.
Precompiled k8 binaries for Mac and Linux can be found at the [K8 release Precompiled k8 binaries for Mac and Linux can be found at the [K8 release
page][k8]. 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`. eyeballing. PAF has to be generated with minimap2 option `-S`, which writes
the aligned sequences to the `cs` tag.
* [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
number of long gaps. This scripts seamlessly works with both SAM and PAF. number of long gaps. This scripts seamlessly works with both SAM and PAF.
* [pbsim2fa.js](pbsim2fa.js): convert reads simulated with [PBSIM][pbsim] to * [pbsim2fa.js](pbsim2fa.js): convert reads simulated with [PBSIM][pbsim] to
FASTA and encode the true mapping positions to read names. FASTA and encode the true mapping positions to read names in a format like
`S1_33!chr1!225258409!225267761!-`.
* [pbsim-eval.js](pbsim-eval.js): evaluate mapping accuracy for FASTA generated * [pbsim-eval.js](pbsim-eval.js): evaluate mapping accuracy for FASTA generated
with [pbsim2fa.js](pbsim2fa.js). This script only works with PAF. For SAM, with [pbsim2fa.js](pbsim2fa.js). This script only works with PAF. For SAM,
please run the following instead: please convert to PAF first:
```sh ```sh
k8 sam2paf.js -p aln.sam | k8 pbsim-eval.js /dev/stdin k8 sam2paf.js -p aln.sam | k8 pbsim-eval.js /dev/stdin
``` ```