Comparing Transcriptome Assemblers for 454 Data
Author Information
Author(s): Sujai Kumar, Mark L Blaxter
Primary Institution: Institute of Evolutionary Biology, University of Edinburgh
Hypothesis
Which assembler provides the best results for transcriptome data from non-model organisms?
Conclusion
Newbler 2.5 performed best overall, but combining different assemblers yielded better results.
Supporting Evidence
- Newbler 2.5 produced the longest contigs and best alignments.
- SeqMan had the most novel sequences but generated many redundant contigs.
- Merging assemblies improved alignment to reference sequences.
Takeaway
This study looked at different computer programs to put together DNA sequences from a parasite, finding that using more than one program can give better results.
Methodology
The study systematically compared five assemblers using a new dataset from the parasitic nematode Litomosoides sigmodontis.
Limitations
No single assembler was optimal for all criteria, and the study focused on a specific dataset.
Participant Demographics
The study focused on the parasitic nematode Litomosoides sigmodontis.
Digital Object Identifier (DOI)
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