Re: [wgs-assembler-users] Can one Rerun scaffolding with fewer libraries

[Brian W. <th...@gm...>]

Hi, Geoff-

Yes.

Make a new run directory, symlink the 0-6 directories, and copy the smaller
files in gkpStore.  The first y.pestis example shows how to copy gkpStore
for this.

http://wgs-assembler.sourceforge.net/wiki/index.php/Yersinia_pestis_KIM_D27,_using_454_8_Kbp_mated_reads,_with_CA8.2

On the gkpStore copy, edit to remove the mate ID from each read in that
library.  Something like:

"gatekeeper -dumpfragments -randommated <lib> 1.0 -tabular *gkpStore >
mated-reads-in-lib" to get a list of the reads in the library, then edit
that list of reads to look like:

frg iid <iid> mateiid 0
...

then gatekeeper -edit <file> *gkpStore

The bottom of http://wgs-assembler.sourceforge.net/wiki/index.php/GkpStore
has the docs for this.

Restarting runCA on this new directory should pick up with CGW.  Results
won't be identical to a fresh start, as the insert size on the other
libraries is already set.  You could edit those back to the original.  The
impact will be small, I think.

b


On Thu, Dec 11, 2014 at 10:47 AM, Waldbieser, Geoff <
Geo...@ar...> wrote:

>  Hi,
>
> I have completed an large assembly using a combination of PE reads and
> jump reads, and would like to compare this with an assembly that does not
> utilize the longest jump library. However this  is a large assembly with a
> long runtime. Can one utilize the data from prior stages and rerun cgw and
> the downstream processes but remove the particular library from the
> scaffolding process?
>
>
>
> Geoff
>
>
>
>
>
> Geoff Waldbieser
>
> USDA, ARS, Warmwater Aquaculture Research Unit
>
> 141 Experiment Station Road
>
> Stoneville, Mississippi 38776
>
> Ofc. 662-686-3593
>
> Fax. 662-686-3567
>
>
>
>
>
>
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