Easy to use Parallel Lastz script
- python 3.x (3.7.7 tested)
- Biopython
- samtools
- lastz
conda create -n plastz
conda activate plastz
conda install biopython lastz samtools
Using requirements.txt
conda create -n plastz --file requirements.txt
Any alignment:
python PlastZ.py <query> <target> <outdir> --lastz-options <"quoted string"> --processes <INT>
Self-alignments:
python PlastZ.py <query> <query> <outdir> --lastz-options <"quoted string"> --processes <INT>
Exemple:
python PlastZ.py reads.fa reference.fa read_aligned/plastz_out -p 10 \
-lo="--format=general:ngap,nmismatch,name1,size1,length1,start1,end1,name2,size2,length2,start2,end2,identity"
Depending on the output format, multiple headers may be found in the output single alignement file!
Self alignments with Plastz may result differently from the command lastz query\[multiple\] --self
This script only launches many parallel Lastz alignments, using it with many sequences will help improve runtime but is still not as efficient as using another multithreaded software.