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Moving forward, developing computational methods and pipelines that integrate results from mapping- and sequencing-based platforms, or better, leverage raw datasets to improve sequencing pipelines, will help us learn more about whole genomes.
The KAPA Stranded RNA-Seq Kit with RiboErase uses a targeted enzymatic depletion method to remove ribosomal RNA (rRNA) and thereby improve sequencing efficiency.
For the paraffin-embedded assays that did not performed as well as their frozen counterparts (specifically exons from genes TP53 and GATA3), PCR conditions as well as their primers were modified to improve sequencing.
The next-generation sequencing (NGS) technologies improve sequencing depth and render large-scale EST projects more feasible [ 25- 27].
In addition, the reverse primer HrU10-EXT-R2 (5'-GCTGCTGTTCGAGGAAATAA-3') was designed to improve sequencing of tree swallow alleles.
Development of a computational methodology may improve sequencing efficiency with this method, through optimisation of 5-methyl-dCTP concentration and prediction of coverage for each nucleotide.
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For example, Mann et al. [18] presented a semi-supervised CRF to improve sequence segmentation and labelling.
Standard and long range PCR was used to close gaps, improve sequence quality and resolve any remaining base-conflicts.
To improve sequence coverage, we used a size selection procedure that removed cDNAs shorter than 1.3 kb in length.
Additional directed sequencing was performed as necessary to improve sequence quality genome-wide to a minimum base call error rate of 1 in 10,000 (i.e. Q40).
Although we did not systematically test this due to the cost per experiment, avoiding DNA exposure to ultraviolet light seemed to substantially improve sequence quality.
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