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Secondly, the highly uneven read coverage and an increased proportion of chimeric reads can be caused by the MDA procedure.
Sequence reads can be assembled either by anchoring them directly onto an available reference genome (classical reference assembly), or can be concatenated by overlap (de novo assembly).
In alternative, raw reads can be also used for direct assignment and annotation, though their short length may limit the exhaustivity of the results.
Alternatively, additional reads can be produced by simply sequencing a sample multiple times.
In S1, 32.8% reads can be mapped to the reference plasmid genomes or certain regions of the chromosome genome.
An additional challenge is that, for new genomes or material from an unidentified source, there may be no reference available against which the reads can be checked.
First, the unaligned reads can be assembled into contigs.
The associated reads can be found under SRA096061.
Further to graph structure, the attributes of the sample and sampled sequence reads can be used.
After clustering, the accuracy of mapping short reads can be improved.
Sequence reads can be quality assessed and filtered using FASTX [ 28].
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