Re: [wgs-assembler-users] Question about contaminant trimming and referring quality value

[Liu, X. <xy...@so...>]

To run Consed while bypassing phd files you can run "consed -nophd". But as Brian pointed out it might crash with big assemblies. Another assembly viewer I used to run on CA assemblies is Hawkeye (http://amos.sourceforge.net/wiki/index.php?title=Hawkeye).

Best,
Jerry

________________________________
From: Brian Walenz [th...@gm...]
Sent: Friday, March 13, 2015 10:13 PM
To: Takashi Koyama
Cc: wgs...@li...
Subject: Re: [wgs-assembler-users] Question about contaminant trimming and referring quality value

I'll be no help on visualization.  Most of the things I've assembled were too big for that.

For trimming, the assembler will do a respectable job without cleaning up vector.  Reads with both vector and genomic sequence will look like chimera, and will have the smaller portion removed.  Reads of entire vector will assemble together, and will need to be screened from the output.  Mate pairs across the junction (one read vector, one read genomic) are a potential problem, and could confuse the scaffold graph enough to prevent assembly.

If you have high coverage Illumina, mapping to the ecoli/vector and discarding the entire pair for any hit is the simplest and safest.  Bowtie2 will do this, but I forget the option.

It's been a long time since I've had to clean up Sanger reads, and hopefully I can continue forgetting how to do it.

In all cases, your best bet is to hard trim -- remove the vector/ecoli sequence from the reads -- before giving the reads to the assembler.  Don't pass in a clear range to the assembler, as it will probably ignore it.

b


On Fri, Mar 13, 2015 at 9:18 AM, Takashi Koyama <tak...@gm...<mailto:tak...@gm...>> wrote:
Hello, I have two questions.

First question. I now trying to assemble BAC clones. As BAC samples include BAC vector and some of E. coli genome, assemblers I've ever used refer vector and E. coli fasta sequences to trim them. However, I could not find an instruction to do that in celera assembly.
Is it possible to refer some fasta files for trimming in CA? Or if impossible, could anyone tell me how I trim them in CA?

Second question. I would like to see how good CA works by assembly viewer. I usually use Consed. I could get an ace file using ca2ace.pl<http://ca2ace.pl> and open it in Consed. However, Consed told me there is no quality files such as phd file. Could anyone tell me any solutions making Consed work smooth?

Thank you for your kind helps.

TK

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