Our goal in developing a best practice pipeline is to produce most contiguous, error-free and complete transcriptome assemblies given these challenges. ![]() Transcriptome assemblers, unlike genome assemblers, must handle the wide range of depth of coverage due to gene expression variation. Some of the factors that lead to this fragmentation are sequencing errors, polymorphism, sequence repeats, and for more lowly expressed transcripts, stochasticicty of read depth that leads to gaps in coverage. While this makes the assembly process computationally tractable, it can lead to fragmented assemblies of a large number of contigs that are subsequences of the underlying true transcripts. Thus, de novo transcriptome asssemblers use DeBruijn graphs, which are constructed and extended based upon kmers, i.e. While early genome assemblers used pairwise overlaps between long reads to extend contigs, this approach is unfeasible when dealing with hundreds of millions of reads. Published on Tue 29 September 2020 Modified Fri 05 March 2021ĭespite a steady increase in the availablity of tools and documented pipelines for building transcriptome assemblies, de novo transcriptome assembly from relative short Illumina paired-end reads remains an extremely challenging endeavor.
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