Question: Is Their Any Good Tool For The De Novo Assembly Of Chimeric Reads
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gravatar for Raghav
6.0 years ago by
Raghav100
Allahabad, India
Raghav100 wrote:

Hello you all, I am looking for good de novo assembly tool for illumina paired end reads [100 nt long],

Your suggestions are always welcome. Thank you

ADD COMMENTlink modified 6.0 years ago by Vivek2.3k • written 6.0 years ago by Raghav100
1

how do you know your reads are chimeric? Are you sure that you are using chimeric in the correct sense?

ADD REPLYlink written 6.0 years ago by Michael Dondrup46k

Dear, Michael First I tried to mapped entire reads on reference and then filter chimeric reads only. yes, I am sure. if you have any suggestion regarding this then your are most welcome.

ADD REPLYlink written 6.0 years ago by Raghav100
1

[100 nt long] should be [100 bp long]

ADD REPLYlink written 6.0 years ago by Tky990

thnQ for correcting it.

ADD REPLYlink written 6.0 years ago by Raghav100
1

Are you talking about chimera potentially resulting from a PCR step? In that case, you should think about filtering out those which are detected using an algo such as, e.g. uChime http://drive5.com/usearch/manual/uchime_algo.html before the assembly step.

ADD REPLYlink written 6.0 years ago by Manu Prestat3.9k
2
gravatar for Vivek
6.0 years ago by
Vivek2.3k
Denmark
Vivek2.3k wrote:

It depends on the genome size and insert sizes of the reads. For larger genomes, if you have one overlapping insert library and another large insert library, you can use ALLPATHS which has inbuilt error correction mechanism that can handle chimeric reads. Otherwise you have SOAP-Denovo, which is pretty efficient but you need to develop your own error correction scripts to remove chimeric reads before assembly.

ADD COMMENTlink written 6.0 years ago by Vivek2.3k

Dear Vivek, ThnQ for the suggestion, I think SOAP-Denovo is realy good one for de novo assembly.

ADD REPLYlink written 6.0 years ago by Raghav100
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