Question: Tools For De Novo Transcriptome Assembly Of Hybrid 454+Illumina Reads?
1
gravatar for Ahdf-Lell-Kocks
7.2 years ago by
Ahdf-Lell-Kocks1.6k
Ahdf-Lell-Kocks1.6k wrote:

Are there any good tools for de novo transcriptome assembly of hybrid 454+Illumina reads?

illumina rna transcriptome • 3.2k views
ADD COMMENTlink modified 4.4 years ago by Leandro de Mattos90 • written 7.2 years ago by Ahdf-Lell-Kocks1.6k
4
gravatar for Rt
7.2 years ago by
Rt80
Rt80 wrote:

This post provided the following 8 choices:

  1. Assemble 454 data on its own and correct with Illumina data
  2. Perform a hybrid assembly with MIRA
  3. Perform a hybrid assembly with CLC Genomics Workbench
  4. Perform a hybrid assembly with … Seqman Ngen/RAY/Celera Assembler/other
  5. Assemble Illumina data and 454 data separately and combine with MINIMUS
  6. Fake Sanger reads from 454 or Illumina assembly and feed to the other assembler
  7. Local assembly of abundant paired-end data to fill 454 scaffolds
  8. Newbler 2.6, incorporating FASTQ files

Personally I may try option 5, 8 and 2.

ADD COMMENTlink written 7.2 years ago by Rt80
2
gravatar for Lee Katz
7.2 years ago by
Lee Katz2.9k
Atlanta, GA
Lee Katz2.9k wrote:

I know of Oases in the Velvet package, but I have no idea how good it is. Good luck!

ADD COMMENTlink written 7.2 years ago by Lee Katz2.9k
1
gravatar for Jbridgers
7.2 years ago by
Jbridgers10
Jbridgers10 wrote:

MIRA might be a good option as well

http://sourceforge.net/apps/mediawiki/mira-assembler/index.php?title=Main_Page

ADD COMMENTlink written 7.2 years ago by Jbridgers10
0
gravatar for Leandro de Mattos
4.4 years ago by
Brazil
Leandro de Mattos90 wrote:

Hi, everyone. I obtained the contigs of a genome of NCBI (of 454 sequencing) and I want to improve the coverage of this genome sequenced, for this I obtain the genome sequencing using illumina (pair-end). I would like to map the reads generated in Illumina in the contigs and improve the coverage of this genome. In mira, Can I use contigs Instead of reads? Because I'don t have the reads of 454 in fastq format. Please, Thank you for any help.

ADD COMMENTlink modified 4.4 years ago • written 4.4 years ago by Leandro de Mattos90
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