what is the mean about c and a parameters? about arcs HOT 3 CLOSED

Hi @sunnycqcn,

c is an ARCS parameter, while l and a are LINKS parameters. The respective help pages describe what they do:

   -c, --min_reads=N     min aligned read pairs per barcode mapping [5]

This means that at least c read pairs of a barcode must map to a contig end before ARCS considers that the barcode hits to that contig end.

-l  minimum number of links (k-mer pairs) to compute scaffold (default -l 5, optional)
-a  maximum link ratio between two best contig pairs (default -a 0.3, optional)
	 *higher values lead to least accurate scaffolding*

Both of these parameters control how LINKS traverses through the scaffold gap, and merges sequences.
In the case of ARCS, there must be at least l barcode links between the contigs for LINKS to consider merging them. In addition, when LINKS is extending a contig using the scaffold graph, and it comes to a point where there are multiple possible contigs to extend to, it uses a to determine if the link with the highest # supporting barcodes is most dominant. If checks if (# links with second-best neighbour)/(# links with best neighbour) < a. There is more detail about these parameters and and an example on the LINKS github page (https://github.com/bcgsc/LINKS)

Lower c, higher a and lower l decrease the stringency of the scaffolding.

Hope that helps!
Lauren

from arcs.

I'll close this for now, but feel free to re-open if you have further questions about the parameters.

from arcs.

from arcs.