Forum: Pipeline for a meta-assembly of De-novo Transcriptome · Biostar

This is a test version of Biostars. For the public version, visit https://www.biostars.org.

Forum: Pipeline for a meta-assembly of De-novo Transcriptome

Hi all,

I'm about to analyze a De Novo transcriptome assembly and I have more than 500GB from different runs (both 454 and Illumina). I was thinking to analyze the 454 with Mira or Newbler and the Illumina with Trinity. Further, merging all the obtained contings using CAP3. What do you think? Does anyone have any experience with co-assembly?

Thanks!

assembly rna-seq

• 2,576 views • link

updated 3.4 years ago by Ram

• written 11.4 years ago by giorgiocasaburi

0 answers

No answers yet.

Log in to answer this question.

More posts like this

Merging de-novo transcriptome assembly from multiple datasets
written 9.3 years ago by gil.hornung

Hi, I have a new dataset of Illumina RNA-sequencing from an organism without a known genome. I have two more older datasets from the same …
Reduce redundancy of Trinity assembly using MIRA software
written 11.1 years ago by seta

Hi all, As you know Trinity generates too much contigs during de novo transcriptome assembly, as far as I found some people use cd-hit-est tool …
Using generated transcriptome assembly by two assemblers
written 11.1 years ago by seta

<p>Dear all,</p> <p>I performed de novo transcriptome assembly for a non-model plant using two assemblers, CLC genomic workbench and Trinity tool. Both assembly sounds good, …
Transcriptome hybrid assembly 454 + Illumina
written 11.2 years ago by giorgiocasaburi

Hello, I have tons of data (about 1Tb) of RNA-Seq coming from different technologies (i.e. 454 - single end, Illumina both single and paired end) …
Optimizing De Novo Transcriptome assemblies for non model organisms
written 11.4 years ago by giorgiocasaburi

Hi all, I have to analyze 24 transcriptomes (TRM) in order to compare gene expression in different conditions of an animal, which genome has not …
Futher analysis on Trinity fasta output
written 11.7 years ago by Whoknows

Hi friends, I used Trinity assembler for de-novo assembly of a plant transcriptome based on same group protocol *"De novo transcript sequence reconstruction from RNA-Seq: …
Cap3 Integration Of Velvet And Newbler Assemblies
written 13.7 years ago by tommivat

<p>I am conducting de novo assembly of ~33Mb genome using 454 and Illumina reads. I cannot use MIRA, since I have ~80M Illumina reads (would …
Hybrid Assembly Transcriptome - Hiseq And 454
written 14.3 years ago by User 8662 •

<p>hi</p> <p>i am working on a rna seq dataset which was sequenced PE with 454 and Hiseq. I have assembled 454 with newbler and hiseq …
De Novo Transcriptome Assembly Options For Mixed Platforms (454, Sanger, Solexa)
written 14.4 years ago by Jlw

<p>Looking for some information on assemblers that can work with mixed data for de novo assembly of <strong>transcriptomes</strong></p> <p>I currently have independent assemblies of RNA-Seq …
A Question About Hybrid Assembly
written 15.2 years ago by Lhl

<p>Hi there,</p> <p>I have some sequence (reads) data produced by both 454 and illumina technologies. And i assembled the 454 reads using Newbler, and illumina …