Skip to content
A C++ wrapper for minimap2
C C++ Makefile
Branch: master
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
src
test
.gitignore
Makefile
README.md

README.md

mm2wrapper

C++ wrapper for minimap2

Description

minimap2 is a versatile pairwise aligner for genomic and spliced nucleotide sequences written in C. The goal of this project is to write C++ wrapper for this tool in order to incorporate it into Flye.

In src/example.cpp you can find an usage example of minimap2 API with C++ interface. The example shows how to build an index and how to use this index to find overlaps for pacbio reads.

Requirements

  • GCC 4.8+
  • GNU make

Installation

git clone https://github.com/EvgenyPolevikov/mm2wrapper
cd mm2wrapper && make

Usage example

./mm2wrapper test/ecoli-pb-first10.fasta test/ecoli-pb-first10.fasta > ovl.paf
head ovl.paf
seq1    6709    3       6708    +       seq1    6709    3       6708    6705    6705    0
seq2    2820    8       2818    +       seq2    2820    8       2818    2810    2810    0
seq3    12187   8       12183   +       seq3    12187   8       12183   12175   12175   0
seq4    11468   2       11464   +       seq4    11468   2       11464   11462   11462   0
seq4    11468   10044   11427   -       seq5    2020    46      1429    232     1383    0
seq4    11468   10286   11192   -       seq5    2020    275     1181    174     906     0
seq4    11468   10047   11419   -       seq5    2020    53      1425    152     1372    0
seq4    11468   10330   11207   -       seq5    2020    261     1138    137     877     0
seq4    11468   9803    10010   -       seq5    2020    1469    1676    127     207     0
seq4    11468   10767   11285   -       seq5    2020    189     707     125     518     0
You can’t perform that action at this time.