search

shingocat / lrscaf

TGS scaffolding
45 stars 6 forks source link

Contig used more than once ? #18

Closed ptranvan closed 4 years ago

ptranvan commented 4 years ago

Hi, we found some contigs that were used more than once in the scaffolding. For instance ctg015357 which is in scaffolds G824 and G7782.

cat nodePaths.info

digraph G824{
ctg038297->ctg044989->ctg015357->ctg028040->ctg034934->ctg075623->ctg055892->ctg000373;

digraph G7782{
ctg014392->ctg015357;

How is it possible and what is your interpretation about that ?

Thanks.

shingocat commented 4 years ago

Hi ptranvan,

By using read coverages information, LRScaf determine the repeat contigs or unique contigs. If it is the type of repeat contigs, it will use more than one in the graph travel.

ptranvan commented 4 years ago

Thanks @shingocat.

It makes sense. Is there any option to use a contig uniquely (even if it's a repeated one) ?

shingocat commented 4 years ago

Hi ptranvan,

There is no parameter for this purpose now.