Welcome to minimappy’s documentation!¶
Python bindings to minimap2 aligner; sufficient to load and index and perform alignments of sequences to the index to obtain basic statistics.
These python bindings are licensed under Mozilla Public License 2.0, minimap is licenced under The MIT License.
Installation¶
The git source repository contains minimap2 as a submodule. The repository should therefore be cloned using the recursive option.
The package setup.py script requires libminimap2.a to have been built in the submodule directory before running. This can be performed via the libminimap2.a target. To build and install the package one should therefore run:
git clone --recursive https://github.com/nanoporetech/minimappy.git
make minimap2/libminimap2.a
python setup.py install
Performing Alignments¶
The MinimapAligner class provides a pythonic interface to minimap2 aligner. It takes as input minimap index or reference .fasta on construction and can then be used to find alignments of sequences given as strings:
from minimappy import MinimapAligner
index = 'path/to/index' # the path given to minimap index
seq = 'ACGATCGCGATCGA'
aligner = MinimapAlinger(index)
alignments = aligner.align_seq(seq)
print('Found {} alignments.'.format(len(alignments))
for aln in alignments:
print(' ', aln)
The alignments are returned as a named tuple, e.g.:
Alignment(rname='yeast', orient='+', pos=0, mapq=60, cigar='915M3D29M3D27M3D13M', NM=12, flag=0)
Alignment parameters can be given as they are on the minimap2 command line:
from minimappy import MinimapAligner
index = 'path/to/index'
options = '-x ont2d -A 1 -B 0'
aligner = MinimapAligner(index, options=options)