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?
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)
But such things are not documented… 😛 @bkille @AndreaGuarracino
It seems I just used the wrong tool for plotting. Above the plot including base pair level alignments. From my observations so far, changing
-nfor 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.