AnchorWave on a very repetitive plant genome

[agolicz]

Hi, I have been testing AnchorWave (v1.0.1) on a very repetitive plant genome (Faba bean, 13 Gb), but the run time has been extremely long. Alignement of a single chromosome (chr1L) has been running for over 3 day now. Do you perhaps have any recommendations?

anchorwave gff2seq -i chr1L.gff3 -r seq2.fa -o cds.fa
minimap2 -x splice -t 10 -k 12 -a -p 0.4 -N 20 seq2.fa cds.fa > ref.sam
minimap2 -x splice -t 10 -k 12 -a -p 0.4 -N 20 seq1.fa cds.fa > alt.sam
genoAli -t 5 -i chr1L.gff3 -as cds.fa -r seq2.fa -a alt.sam -ar ref.sam -s seq1.fa -v alt.vcf -n alt.anchors -o alt.maf -f alt.f.maf > alt.log
cat alt.log
reading reference sam begin
reading reference sam done
using parameters detected from the input SAM file for novel anchors identification

The data can be found here: https://projects.au.dk/fabagenome/genomics-data