Tools For De Novo Transcriptome Assembly Of Hybrid 454+Illumina Reads?

Question

[Ahdf-Lell-Kocks]

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

[Leandro de Mattos]

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.

[jthoward93]

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.

[ATpoint]

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

Answer 1

[Rt]

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.

Answer 2

[Lee Katz]

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

Answer 3

[Jbridgers]

MIRA might be a good option as well

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