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Does anybody know an opensource software package for whole genome assembly of cDNA with Illumina paired-end sequencing? I'm really looking for an assembler designed for cDNA data, not DNA. I don't think that programs like Velvet or SSAKE can deal with this kind of data (I may be wrong). MIRA seems OK but it is not quite clear whether it takes the "paired-end" feature into account when assembling cDNA data. Any help is much appreciated !!
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I don't understand your question - cDNA is just a small part of a whole genome. Are you talking about an EST assembly of the transcriptome (i.e. extract mRNA, covert to cDNA, sequence it, assemble it).
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Thx Zigster. Yes I mean the transcriptome assembly. After some research, it seems that MIRA can deal with this kind of data (EST + paired end + short read). I saw in several papers that CAP3 was used on the assembled contigs (to get larger contigs). Is this a good idea ? Do you have any advice ?Comment
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if you have 100M short reads I would give those to Velvet and then use those contigs in an alignment based program like you mentioned
i like Mira but the parameter setup is a hassle. Prepare to set aside a couple hours to read the manual.Comment
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...06-18-2026, 07:11 AM -
Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...06-02-2026, 10:05 AM
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