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Uneven abundance ratios in metagenomic data introduce another problem in assembly, because existing assemblers cannot distinguish erroroneous reads sampled from genomes with high abundance ratios and reads from genomes with low abundance ratios.
Sequence planning is an important problem in assembly line design.
Shorter read length was a major problem in assembly, especially in case of de novo assembly of the data from novel organisms, which do not have previously assembled and annotated reference sequences [ 18, 19].
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Thus, it is particularly important to address this problem in assemblies with short reads.
Well-to-well contamination causes major problems in assembly.
Although NG sequencing does outperform traditional sequencing in many areas, the problems in assembly cannot be underestimated.
Solexa and SOLiD sequences, currently less than 40 bp, will pose problems in assembly of unigenes, especially for short segments of genes that may be present in several genes.
Ring's deformation in a radial direction is a problem in ring assembly.
Interlayer gap formation during through-hole drilling in stacked structures is a common problem in large assembly operations.
However, the narrow passage which is a common problem in the assembly tasks is still a bottleneck.
A second problem in transcriptome assembly of ciliates that cannot be grown axenically is that there may be mitochondrial as well as bacterial transcript-related reads mixed in RNA-seq data.
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