Question: Tools For De Novo Transcriptome Assembly Of Hybrid 454+Illumina Reads?
1
gravatar for Ahdf-Lell-Kocks
8.5 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 • 3.6k views
ADD COMMENTlink modified 13 months ago by jthoward930 • written 8.5 years ago by Ahdf-Lell-Kocks1.6k

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 REPLYlink modified 5.7 years ago • written 5.7 years ago by Leandro de Mattos90

Here's a paper: https://www.ncbi.nlm.nih.gov/pubmed/22750884

Abstract Single-molecule sequencing instruments can generate multikilobase sequences with the potential to greatly improve genome and transcriptome assembly. However, the error rates of single-molecule reads are high, which has limited their use thus far to resequencing bacteria. To address this limitation, we introduce a correction algorithm and assembly strategy that uses short, high-fidelity sequences to correct the error in single-molecule sequences. We demonstrate the utility of this approach on reads generated by a PacBio RS instrument from phage, prokaryotic and eukaryotic whole genomes, including the previously unsequenced genome of the parrot Melopsittacus undulatus, as well as for RNA-Seq reads of the corn (Zea mays) transcriptome. Our long-read correction achieves >99.9% base-call accuracy, leading to substantially better assemblies than current sequencing strategies: in the best example, the median contig size was quintupled relative to high-coverage, second-generation assemblies. Greater gains are predicted if read lengths continue to increase, including the prospect of single-contig bacterial chromosome assembly.

ADD REPLYlink modified 13 months ago • written 13 months ago by jthoward930

How does this contribute to this 7.4-year old question that was about Illumina/454?

ADD REPLYlink written 13 months ago by ATpoint36k
4
gravatar for Rt
8.5 years ago by
Rt90
Rt90 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 8.5 years ago by Rt90
2
gravatar for Lee Katz
8.5 years ago by
Lee Katz3.0k
Atlanta, GA
Lee Katz3.0k wrote:

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

ADD COMMENTlink written 8.5 years ago by Lee Katz3.0k
1
gravatar for Jbridgers
8.5 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 modified 10 months ago by RamRS28k • written 8.5 years ago by Jbridgers10
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