Re: [wgs-assembler-users] scaffolding with TruSeq synthetic reads

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

Hi-

Sorry, this got lost in the holidays.

Look into masurca (http://www.genome.umd.edu/masurca.html).  It's an
offshoot of CA which handles Illumina PE/MP much better.

To run with CA, I'd suggest:

1) Use all reads from the start.
2) Mark the TruSeq as a non-random library -- I don't trust it to be
random, and if it isn't, repeats will be all messed up.
3) You'll need to use 'dnc' to clean up the mate pair reads.  The TruSeq
should help here.
4) unitigger=bogart
5) Stopping after unitigs (stopAfter=unitigger) and evaluating unitig sizes
(tigStore -g *gkpStore -t *tigStore 1 -U -d sizes) is generally helpful.
6) The 'fragment error correction' module is somewhat helpful, but very
expensive.  Disable it (doFragmentCorrection=0).

http://wgs-assembler.sourceforge.net/wiki/index.php/Pair_classification_within_Illumina_mate_pair_data
http://wgs-assembler.sourceforge.net/wiki/index.php/RunCA#De-novo_Classification

b



On Fri, Jan 2, 2015 at 6:56 PM, Doyle, Jacqueline R M <jm...@pu...>
wrote:

>  Hi!  I’m working on an assembly of a non-model avian genome.  We
> currently have Illumina paired-end reads that I’d like to use for
> contig-building, as well as both a mate-pair library and low coverage
> Illumina TruSeq synthetic reads (formerly Moleculo) that I’d like to use
> for scaffolding.  Is this possible (and advisable) with Celera?
>
>
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