What are the most important factors to get the full length contigs during de novo transcriptome assembly?

Question

[seta]

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

Answer 1

[Antonio R. Franco]

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