Question: How To Merge Contigs From Two Different Assembler :
4
gravatar for HG
5.4 years ago by
HG1.1k
Germany
HG1.1k wrote:

HI everyone, I am new in genome assembly. I did my Denovo assembly with Spades( SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing) and i also did the assembly with GapFiller (GapFiller: a de novo assembly approach to fill the gap within paired reads) .

Now if i merge the contig file from both the program which program i can use for this job??

After merging the contig the quality of draft genome will increase or not ??

If any one have experience please help me out ..

Thank you advance

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ADD COMMENTlink modified 5.4 years ago by Hranjeev1.5k • written 5.4 years ago by HG1.1k
3
gravatar for Hranjeev
5.4 years ago by
Hranjeev1.5k
Malaysia
Hranjeev1.5k wrote:

We have tried GAM-NGS and obtained good results. But I'm afraid your method is not appropriate because gapfiller is used after scaffolding step, if I'm not wrong. You should try to merge contigs from abyss, velvet etc. with your SPADES contig results.

Reference: GAM-NGS: genomic assemblies merger for next generation sequencing

Other tools I know off using similar species references:

ADD COMMENTlink modified 5.4 years ago • written 5.4 years ago by Hranjeev1.5k

I appreciate your opinion . Current i have two set of contig file one from spades and another from Masurca , now i just want to check the change of N50 value if i can merge these two set. Any suggestion ???

ADD REPLYlink written 5.4 years ago by HG1.1k

I believe the N50 can be improved with GAM-NGS. Please try and let us know.

ADD REPLYlink written 5.4 years ago by Hranjeev1.5k

thanks .......let me check once ...then i will let you know

ADD REPLYlink written 5.4 years ago by HG1.1k
1
gravatar for HG
5.4 years ago by
HG1.1k
Germany
HG1.1k wrote:

As you suggested i am using minimus2 like this way :

$grep -c "^>" S1.seq S2.seq
   S1.seq:917
   S2.seq:1668

 $ cat S1.seq S2.seq > S1-S2.seq
 $ toAmos -s S1-S2.seq -o S1-S2.afg
 $minimus2 S1-S2 -D REFCOUNT=917

Finally i got one file named "S1-S2.afg" could you please let me know what will be next step to get contig merge fasta file??

ADD COMMENTlink modified 5.4 years ago • written 5.4 years ago by HG1.1k

I'm not a minimus2 expert. However have you tried to simply type:

minimus2 S1-S2.afg

?

By the way, I've found a new tool thanks to excellent didactic directory OMICtools : I edit my answer.

ADD REPLYlink modified 5.4 years ago • written 5.4 years ago by Manu Prestat3.9k

Did you figure it out? minimus2 (from amos 3.1.0) does not need the ".afg" extension explicitely described

Having said that, I noticed that minimus2 has a configuration bug: it assumes that MUMmer executables deltafilter and show-coords are under /usr/local/bin. A simple modification of that will solve the problem.

ADD REPLYlink modified 2.3 years ago • written 2.6 years ago by Israel Barrantes740
0
gravatar for Manu Prestat
5.4 years ago by
Manu Prestat3.9k
Marseille, France
Manu Prestat3.9k wrote:

Take a look at minimus2.

EDIT: and GARM.

ADD COMMENTlink modified 5.4 years ago • written 5.4 years ago by Manu Prestat3.9k

I tried GARM but failed with the error message: 

ERROR: A MUM was found with a start coordinate greater than
       the sequence length, a serious error has occured.
       Please file a bug report
ERROR: postnuc returned non-zero

and

ERROR: mummer and/or mgaps returned non-zero

I've tried complie Mummer 3.22 & 3.23 with make CPPFLAGS="-O3 -DSIXTYFOURBITS", but the problem remained. Do you have any suggestions?

ADD REPLYlink written 5.0 years ago by zy04122560
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