wfmash: too many alignments with v0.12.6

Hi developers 😃

running

wfmash \
    scerevisiae8.fasta.gz \
    scerevisiae8.fasta.gz \
     \
    --threads 4 \
     \
    -n 7 -s 5000 -p 90.0  -X  -l 25000 -k 19 -H 0.001   -2 30 > scerevisiae8.fasta.gz.paf    

It seems I am getting too many alignments?

out

I would have expected to only get the diagonal output in an all-vs-all setting, right? Or am I missing something?

Best, Simon

About this issue

  • Original URL
  • State: open
  • Created 4 months ago
  • Comments: 20 (17 by maintainers)

Most upvoted comments

But such things are not documented… 😛 @bkille @AndreaGuarracino

scerevisiae8 fasta gz paf

It seems I just used the wrong tool for plotting. Above the plot including base pair level alignments. From my observations so far, changing -n for this data set didn’t change the mappings according to the pafplot.

So PanSN-spec mandatory? Why -n 1? You make nf-core/pangenome unhappy.