Question: What are the most important factors to get the full length contigs during de novo transcriptome assembly?
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gravatar for seta
3.6 years ago by
seta1.3k
Sweden
seta1.3k wrote:

Hi all,

As we all know, getting as much as possible the full-length contigs is desirable during the de novo transcriptome assembly of a non-model organism. Besides to K-mer size and the sequencing depth, what are the most important factors to get the full-length contigs during de novo transcriptome assembly in your opinion?

Thanks

ADD COMMENTlink modified 3.6 years ago by Antonio R. Franco4.5k • written 3.6 years ago by seta1.3k
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gravatar for Antonio R. Franco
3.6 years ago by
Spain. Universidad de Córdoba
Antonio R. Franco4.5k wrote:

A high coverage with a sequencer able to give you very long reads that avoid the use of PCR (to avoid the out of phase error). Sort of a improved version of PacBio with a higher throughout and a lower error rate

Everything else will lead to draft versions of the genomes and this includes the use of Illumina and mate paired reads, or the combination of Illumina or ion torrent reads with long reads

ADD COMMENTlink modified 3.6 years ago • written 3.6 years ago by Antonio R. Franco4.5k
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