minialign

Minimalistic aligner which uses Minimap for input mapping locations and Edlib (Myers' bit-vector impl.) for alignment.

Build

make modules && make tools & make  

Example

./wrap-minialign.sh test-data/lambda/NC_001416.fa test-data/lambda/reads.fastq out.sam  

Usage

Generate a mapping PAF/MHAP file using Minimap, GraphMap or MHAP:

minimap test-data/lambda/NC_001416.fa test-data/lambda/reads.fastq > test-data/lambda/overlaps.paf  

Align the mappings using Minialign:

bin/minialign test-data/lambda/NC_001416.fa test-data/lambda/reads.fastq test-data/lambda/overlaps.paf > test-data/lambda/alignments.sam  

If your mappings are in the MHAP format, you can specify this using the --mhap option.

To use hard-clipping for reporting alignments instead of soft:

bin/minialign --hard-clip test-data/lambda/NC_001416.fa test-data/lambda/reads.fastq test-data/lambda/overlaps.paf > test-data/lambda/alignments.sam