RNAseq assembly for diploid genome.

Question

[Ric]

Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes. Is there anything for RNAseq assembly?

Thank you in advance.

Mic

[Amitm]

You mean de novo? Have you seen Trinity and Trans-Abyss ?

[Ric]

Yes, I saw Trinity and just wondering how to make assembly less fragmented by following steps:

• redundancy reduction: detection and selectively removal of redundant contigs from an initial de novo assembly
• scaffolding: joining of genome fragments using paired-end and/or mate-pairs reads
• gap closing

Redundans pipeline assists an assembly of heterozygous genomes. Program takes as input assembled contigs, paired-end and/or mate pairs sequencing libraries and returns scaffolded homozygous genome assembly, that should be less fragmented and with total size smaller than the input contigs. In addition, Redundans will automatically close the gaps resulting from genome assembly or scaffolding

Answer 1

[Whoknows]

Hi Ric,

You could use Trinity for assemblying RNA-SEQ short reads, trintiy will give you unigene but you'll need to do further analysis on its output. You should then cluster those output sequences by CD-HIT-EST.