Hello, I was wondering with IDBA-Tran they want you to have a .fasta file as input. I converted my file from .fastq to .fasta but I noticed in their example conversion they also filter out reads with NNNs in them. How important is this for proper assembly of the transcriptome? Thanks.
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It is always an option to clean your reads of NNN and other low quality reads, but you don't need to, for this and other assemblers. De-novo assemblers do internally use higher quality reads instead of poor ones where available. I do both ways sometimes, but current Illumina sequencer outputs are generally high quality.
I get good transcript assemblies with idba-trans, with a caveat that I use all the kmer-set "transcripts-kk.fa" outputs, rather than IDBA's final "merged" set, which has poorer gene completeness than the per-kmer sets.
Find here a comparison of 4 gene assemblers, used in EvidentialGene's production of highly accurate gene reconstructions for the malaria mosquito and yellow fever/Zika mosquito:
idba_trans comes in second best, after velvet/oases the reigning champion of gene assembly. idba_trans uses less memory and runs faster than velvet/oases, and the authors' paper helps explain why it and velvet/oases do so well with multi-kmer constructions of the variably expressed genes and their alternate transcripts. Please consider using http://eugenes.org/EvidentialGene/ methods along with several gene assemblers to obtain highly accurate animal and plant gene sets.
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The immune system’s power comes from its genetic diversity, allowing myriad threats to be neutralized through first recognizing foreign antigens. That diversity is also what makes the immune system so difficult to study. Recent advances in sequencing technology and computational biology, however, are giving researchers new tools to understand immune responses and immune-related diseases in greater detail.
This convergence of genetics, immunology, and computation...09-01-2026, 05:41 AM
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