Question: Abyss Single End
0
gravatar for Chestnto
8.7 years ago by
Chestnto0
Chestnto0 wrote:

hi everybody I'm working whit 454 single end sequences obtained from two different species. I need to compare the two thesis. Until now i used Abyss tools, for each one, in the following order: ABYSS with different kmer, abyss-fac to chose the best assembly, Adjlist, popbubbles and mergecontigs. Now which are the best programmes to use to compare the two assembly? Kalign may be? And which commands have i to use? An other question: when i use ABYSS to assembly the sequence i need to use the command se-contig? thank you very much!

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ADD COMMENTlink written 8.7 years ago by Chestnto0
0
gravatar for Darked89
8.7 years ago by
Darked894.2k
Barcelona, Spain
Darked894.2k wrote:

Check the new Abyss manual:

http://www.bcgsc.ca/downloads/abyss/doc/README.html

You may also think about improving the assemblies by performing error correction before the assembly. It did work for me for Illumina reads, but it also has an option for 454:

http://www.cs.helsinki.fi/u/lmsalmel/coral/

As for the assembly comparisons, it depends on quality of your draft assemblies and the level of coverage. If you have any related species with a more accurate genome assembly this will help.

ADD COMMENTlink written 8.7 years ago by Darked894.2k
0
gravatar for ALchEmiXt
8.6 years ago by
ALchEmiXt1.9k
The Netherlands
ALchEmiXt1.9k wrote:

For 454 data I generally consider the Newbler assembler best (just my opinion and some supportive data here). Any reasons to go for ABYSS?

ADD COMMENTlink modified 8.6 years ago • written 8.6 years ago by ALchEmiXt1.9k
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