This is a tool for analyzing lastz alignment result generated using "--format=general" option to find structural variations or to perform super-scaffolding guided by reference genome.
We recommand lastz_32 for large genomes (1>Gbp genome size).
g++ compiler with c++11 (or higher)
lastz (https://github.com/lastz/lastz.git)
Just do
make
After compiling, set PATH
export PATH=/path-to-here/bin:$PATH
or add it into ~/.bashrc or ~/.bash_profile
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Lastz alignment
lastz reference.fa assembly.fa[multiple] --format=general --ambiguous=iupac --step=10000 > output.lastz
If needed, modify --step option, but do not change the option "--format=general". Note that we do not recommand options "--gapped" or "--chain".
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Using lastz_analysis
lastz_analysis -i output.lastz [options] -
Plot
lastz2gnuplot output.lastz [ reference_scaffold_name [ assembly_scaffold_name ] ] > output
If you want noise-filtered one,
lastz2gnuplot output.lastz.filterd chr1 > chr1.plot
If you want generate a plot file of contig_1 to chr1, do
lastz2gnuplot output.lastz.filterd chr1 contig_1 > chr1.contig_1.plot
The output file(s) can be used in gnuplot or R or any other plot tools.
Nise filtered result
(prefix).filter
Default cut-offs are -d 0.985 -l 4000 for noise filtration.
Filtered-out result
(prefix).noise
A summary file with basic statistics of structural variations and options used
(prefix).summary
Structural variation files:
(prefix).delet (Deletion)
(prefix).dupli (Duplication)
(prefix).reduc (Duplication in reference compared with assembly)
(prefix).insrt (Insertion)
(prefix).invrs (Inversion)
(prefix).trans (Inter-chromosomal translocation)
(prefix).reloc (Intra-chromosomal translocation)
Mapping informations
(prefix).map2target (Statistics of mapping status)
(prefix).strand (Strand of assembly scaffold compared with refence)
Strands are calculated in mainly mapped reference scaffold (or chromosome)
Jang-il Sohn
BIG (Bioinformatics and Genomics) Lab.,
Hanyang university, Seoul, Republic of Korea.