Question

Trinity RNASeq DNASeq assembly

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7.3 years ago

nazaninhoseinkhan ▴ 520

Dear all, As a part of my project, I had to assemble whole genome reads of a bacterial species in to contigs.

Unfortunately I had no access to Linux server to run algorithms like Velvet or Abyss.

CLC genomic workbench did not work on my system.

I decided to search for online tools, but even in Galaxy I did not find any algorithm except for Trinity which is a RNASeq assembly program.

As a test I used Trinity to assemble my DNASeq reads.

It produced 80 contigs . When I checked these contigs for Multi Locus Sequence Typing or Drug resistance typing which both are on the basis on alignment, I obtained 100% perfect match.

This somehow assured me that Trinity has assembled my reads correctly.

Now my question is, can I rely on the Trinity results?

I am looking forward your guides

Regards

Nazanin

next-gen Assembly Trinity • 2.4k views

ADD COMMENT • link updated 7.3 years ago by Antonio R. Franco ★ 5.1k • written 7.3 years ago by nazaninhoseinkhan ▴ 520

score 2 · Answer 1 · 2017-02-01

The problem you can face is that Trinity is a transcriptomic assembler that handles the repetitive sequence in a different manner that a genome assembler

For a genomic assembler, reads that are over-represented means repetitive sequences that need to be placed in the genome context

For a transcriptome assembler, over-represented reads simply mean that a determined gene is expressing their transcript at high levels. And try to manage that in a different way

In any case, Trinity will eventually assemble some of your genes, and it will do it right. But it has the tendency to make short fasta files, each of them corresponding to a single gene, whereas the tendency of a genome assembler is to produce long contigs

This is sort of simplified way to explain the differences between the two types of assembler, but hopefully I can give you some important clues about the differences between the two