454ContigGraph.txt

[btully]

The 454ContigGraph.txt file output by the GS assembler is exactly the kind of information I am looking for. However, I could not tell from the Roche manual how to visualize the results. Any suggestions?

[linikujp]

There is detailed introduction in the Version2.3's manual:
Genome Sequencer FLX System Software Manual Part C: GS De Novo Assembler – GS Reference Mapper – SFF Tools
1.15.1.12 454ContigGraph.txt

After you run a cDNA aseembly project, look at the actual file and read the manual. It is clear and easy to understand.

[seqseq]

You are referring to this manual file, right?

http://xyala.cap.ed.ac.uk/Gene_Pool/454_software/Version_2.3/SW-Manual_PartC_Assembler-Mapper-SFFTools_Oct2009.pdf

There is a decription of the "first section" of 454ContigGraph.txt containing the average depth of the alignment per contig. But for the "second section" containing connections between contigs they only describe the lines starting with "C" not the ones starting with "I" or with "F". Does anyone know where I can find a description for these parts of the "second section"?

And does anyone know a way to visualize (parts of) this graph structure?

Thanks

[linikujp]

Yes. It is that manual.

In my file, there are "S" and "I" starting instead of "F" and "I".

Here is an example:
S 1 3694 618:+;561:-;560:+;82:-;711:-;500:+

I 164 AGAGGCTTAgggtttttCATCCAATCaaacAGTGCCAGACCACGGTTACACAACAGAACCGATGGCCTCAGCCGGTAACAGGATGGATACCAacagggtgg
I 502 GC 301:875-3'..855-3';6:970-5'..855-3';2867:971-5'..855-3';5:972-5'..855-3'

Couldn't find the explantation from the manual. I think programmer from 454 can explain this.

[linikujp]

And does anyone know a way to visualize (parts of) this graph structure?

Thanks

You may develop a program to visualize this.
I am thinking of doing this... who else is interested?

[dschika]

I don't know if it is correct but what i suppose looking at my 454ContigGraph-file:

S isotig-id isotig-length contigs_in_isotig(with direction +/-)

I contig_id consenus_sequence coverage-depth:contigs_surrounding_the contig (???) (leading zeros in the contig_id are discarded: 1 = contig00001)

As I'm very unsure about the last entry in the "I-rows" I still don't have a clue why this entry is missing sometimes...

[flxlex]

I got the following explanation:

I: reads 'flowing through' the contig, i.e. reads that start in a neighboring contig, flow through the contig, and end in another neighbor again. In the example:

I 502 GC 301:875-3'..855-3';6:970-5'..855-3';2867:971-5'..855-3';5:972-5'..855-3'

310 reads start in contig 875, flow out it's 3' end, into the 5' of the contig you are looking at (502), out of it again at the 3', and into the 3' of contig 855. The '..' kind of represents the contig in question from 5' to 3'.

In this case, the large number of reads flowing through (301, 6, 2867 and 5, respectively) and the short sequence ('GC') point to a tandem repeat/microsat. All reads go into contig 855, which perhaps is high depth and short also?

[flxlex]

I just posted an entry on the 454ContigGraph.txt file on my blog about newbler:

http://contig.wordpress.com/2010/04/13/newbler-output-iii-the-454contiggraph-txt-file/

Cheers,

flxlex

[linikujp]

I just posted an entry on the 454ContigGraph.txt file on my blog about newbler:

http://contig.wordpress.com/2010/04/13/newbler-output-iii-the-454contiggraph-txt-file/

Cheers,

flxlex

Hi, that's a good one. Thank you!

[lh3]

Thanks. Quite a nice blog on technical details.

[henry.gibbons]

Visualizing 454contiggraph.txt files

You may develop a program to visualize this.
I am thinking of doing this... who else is interested?

I would be very interested in this. You see displays of this at AGBT/other meetings but I have not seen any tools to display this very useful information. I'm not a programmer, so this would be someone else's bag but would love the tool!

[dsenalik]

I would be very interested in this. You see displays of this at AGBT/other meetings but I have not seen any tools to display this very useful information. I'm not a programmer, so this would be someone else's bag but would love the tool!

For anyone finding this old thread, I wrote a program to do just this.

I posted it at this address:

http://www.vcru.wisc.edu/simonlab/sdata/software/index.html#contignet