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The results of all k-mer assemblies were combined with CAP3 to make a line-specific super assembly.
These two assemblies were combined with the 454Isotigs and then clustered with TGICL, resulting in the 'Extended' transcriptome containing 28113 gene clusters and 88078 transcripts.
To increase the length of contigs and reduce the number of redundant contigs the Velvet assemblies were combined with existing sequences from the databases from the publically available Trifolium pratense EST library, downloaded from http://www.plantgdb.org/download/download.php?dir=/Sequence/ESTcontig.
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All contigs and singletons resulting from the Newbler assembly were combined with adaptor-containing reads for input into PTA.
The consensus repeat sequences generated by RepeatModeler for each assembly were combined with the Repbase RepeatMasker library version 20140131.
To improve solar-pumped laser output performance, a compact fused silica light-guide assembly is combined with a 2V-shaped cavity to achieve uniform pumping along a Nd YAG rod.
The contigs longer than 100 bp resulting from the Velvet/Oases assemblies were combined together with 454 contigs for the final assembly with CAP3, to produce what we refer to as the reference library.
The two assemblies were combined to create a more complete genome representation that retained the high quality BAC-based local assembly information, but with gaps between BACs filled in with the WGS-only assembly.
Afterwards, these three assemblies were combined to produce the final non-redundant assembly.
The de novo and genome guided transcriptome assemblies were combined to form a redundant over-assembly.
Afterward, the two sets of assemblies were combined to produce the final nonredundant assembly.
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