Re: arguments for MergeContigs & fachain

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Shaun Jackman

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Dec 4, 2014, 7:01:54 PM12/4/14
to Yifang Tan, ABySS

Hi, Yifang. (cc’ed ABySS mailing list)

MergeContigs should do what you want.

FASTA is the FASTA file of sequences.

OVERLAP is the contig overlap graph describing which sequences overlap and by how much. You can generate this file using AdjList, abyss-overlap or `sga overlap`. The file format is described here:
https://github.com/bcgsc/abyss/wiki/ABySS-File-Formats#dot

You can also use SGA's ASQG format

https://github.com/bcgsc/abyss/wiki/ABySS-File-Formats#asqg

or the emerging GFA (graphical fragment assembly) file format
http://lh3.github.io/2014/07/23/first-update-on-gfa/

http://www.acgt.me/blog/2014/10/15/the-graphical-fragment-assembly-gfa-format

PATH is the identifiers of the overlapping sequences to merge. The file format is described here:
https://github.com/bcgsc/abyss/wiki/ABySS-File-Formats#path

Cheers,
Shaun

On Wed Dec 03 2014 at 7:57:41 AM Yifang Tan yif...@gmail.com wrote:

Hello Shaun!

I am working in NRC in Saskatoon on wheat genome assembly.
What I am trying to do is to merge some overlapping BAC sequences, and I found MergeContigs and fachain in your fastascript bundle seem to be what I need, but I am not sure the arguments:

e.g. for fachain:
$ fachain test.fasta
Use of "goto" to jump into a construct is deprecated at ./fachain.pl line 50, <> line 6.

For MergeContigs function from Abyss 1.5.2, I am not quite sure about those arguments:

  FASTA    contigs in FASTA format
  OVERLAP  contig overlap graph
  PATH     sequences of contig IDs

I could not find any other resource explaining those argument.  Can you please elaborate those a little more?
Appreciate if you could give me some help.
Thank you!


Yifang Tan

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