The Newbler application (version 2.8) in the 454 GS FLX software package (Roche 454 Life Sciences) was used to assemble reads generated from the GS FLX instrument and in combination with reads from the Illumina instrument, as described previously [ 38].
Reads from the 454 platform were assembled separately by using Newbler v2.5.3 (Roche Diagnostics) with its -cdna option, as well as in combination with Illumina reads by using Trinity [ 7] on a server with 256 GB of RAM.
The moderating role of media type (TV in combination with Facebook or reading an online informational website) and the mediating role of state self-esteem were tested.
Huber et al. [115] evaluated the use of single-shot LGE imaging techniques in combination with SSFP read-out in patients with myocardial infarctions and demonstrated excellent correlation of infarct size and volume compared with standard segmented IR techniques.
We evaluated five indel callers in various combinations with read mappers, as shown in Table 1.
The high quality Illumina data in combination with long MinION reads has resulted in a fully circularised, contiguous, and high quality assembly.
Sequences from each BAC were assembled with Phrap, first with just the BAC generated sequences, then in combination with the WGS reads that overlapped the BAC as an enriched BAC (eBAC).
Individual BAC sequences were assembled with Phrap[ 18, 19], first with just the BAC generated sequences, then in combination with the WGS reads that overlap the BAC as an enriched BAC (eBAC).
While we have primarily applied ViennaNGS in combination with the short read aligner segemehl, e.g. in a study addressing ribosome associated mRNA degradation in Drosophila, it has also been used recently with Tophat output in a large scale transcriptome study of Ebola and Marburg virus infection in human and bat cells (Hölzer et al., unpublished data).
The high mapping rate of properly paired Illumina reads, in combination with the high number of mapped MinION reads is indicative of a high quality genome assembly.
We have studied the progress of the phase transition as a function of time by single-crystal diffraction of monochromatic X-rays provided by a synchrotron in combination with a fast read-out CCD based area detector.
