Question: efficient algorithm for de novo assembly using de bruijn graph
gravatar for StudentBio
17 days ago by
StudentBio0 wrote:

hello everebody please I am trying to assemble my reads using an algorithms for de novo assembly( De Bruijn Graph) and I don t know which algorith de novo more efficient in my case the optimal k using kmergenie is 17 Read Data : Ion Torrent, single end, percentage of GC 42, sequence length between 20 and 397

ADD COMMENTlink modified 12 days ago by colindaven740 • written 17 days ago by StudentBio0

What organism is it? How many reads do you have?

You can try SPAdes, which does it's own rounds of kmer optimisation.

ADD REPLYlink written 17 days ago by jrj.healey5.0k

phoenix dactylifera genome length 22 953 390 bp ; het 4,25%

ADD REPLYlink written 16 days ago by StudentBio0

Ususally the is no "better" assembler, and each time you have a new dataset, a different assembler may turn out to be the best. In addition, more information would be useful in getting good suggestions about good assemblers for your case, such as expected genome size, expected sequencing coverage, ploidy and heterozigosity of the organism, among others. For example, some assemblers are optimized for small- or medium-sized genomes (such as SPAdes and MIRA), others are good for large genomes.

Are you assembling several genomes? On a different thread ( choice of k value for mapping my reads again a reference genome ), you found 81 as best kmer acording to KmerGenie.

ADD REPLYlink written 17 days ago by h.mon16k
gravatar for colindaven
12 days ago by
Hannover Medical School
colindaven740 wrote:

Thats a really poor dataset for de novo assembly as it contains only single end reads. Also, Ion torrent data contains lots of nasty indels which cause artificial frameshifts in predicted genes. Lastly, there is no long range information.

What coverage do you have ?

I would advise you to try soap2denovo and Spades. Potentially also Abyss.

By the way, shouldn't the genome be more like 600+ MBp ?

ADD COMMENTlink written 12 days ago by colindaven740
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