Optimising gaps in whole genome assembly alignments

[mnshgl0110]

Hi Winnowmap Team,

I am trying to use winnowmap to do whole-genome alignments. In some cases, winnowmap is resulting in large unaligned regions like below:

However, when I align these unaligned sequence using clustal, they seem to be quite similar.

Do you have any suggestions on how to tweak winnowmap so that these regions can be aligned as well?

My alignment command is:

winnowmap -W TAIR10_k19.txt -x asm5 -t 10 -ac --eqx -r 10000 TAIR10_Filtered.fasta.gz qry.filtered.fa

Thanks
Manish

[cjain7]

If the input sequences are not too big, you could try reducing k-mer size.

[mnshgl0110]

I want to use this with syri for genomic differences identification. The size of the sequences can vary (from A. thaliana (130 MB) to humans to oats (10GB)), so it would be great if there is a solution that can be adopted for different genomic sizes.