In total 30 putative chimeras were identified and removed from the read datasets.
Execution time for mapping different read datasets on different reference genome is shown in Table 2.
PE read datasets with the same read coverage as from SE reads synthesis procedure were generated.
We thank Juliane Dohm and Claudio Lottaz for the idea and scripts about simulation of short reads datasets.
Two strategies were used: the cyanobacterial sxt genes were queried either against the assembled Alexandrium datasets or the unassembled 454 read datasets.
In many cases there are already partial long read datasets which can be leveraged now with the addition of short reads.
We present a simple method, named Rock Band, to exploit sparse long read datasets within a short-read assembly to resolve repeats and extend contigs.
In the present study, eight short reads assemblers, representing four various assembly strategies, were benchmarked against two types of simulated short reads datasets derived from four different genomes.
MetaSim allows the user to simulate individual read datasets that can be used as standardized test scenarios for planning sequencing projects or for benchmarking metagenomic software.
Several algorithms have been developed to more efficiently work with short read datasets [1], [2], [3], but these approaches require costly computing resources to compare each sequence read against all others [1], [2], [3], [4].
However, the downstream analysis of short reads datasets after sequencing is a tough task; one of the biggest challenges for the analysis of high throughput sequencing reads is the whole genome assembly.
