PLastZ

Easy to use Parallel Lastz script

Requirements:

• python 3.x (3.7.7 tested)
• Biopython
• samtools
• lastz

Installation (Bioconda recommended)

conda create -n plastz
conda activate plastz
conda install biopython lastz samtools

Using requirements.txt

conda create -n plastz --file requirements.txt

Quick start

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"

Warning:

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.