Finally, the novel transcripts identified from de novo based assembly pipeline (14,758) and reference-based assembly pipeline (6700) were assembled together using CAP3 assembler.
All other plasmid sequences were assembled together and manually checked for assembly errors.
For example, 20 T. alpinus libraries were assembled together to make species-specific consensus assemblies.
This dataset was constructed to study the extent of co-assembly when reads from very similar organisms are assembled together.
All sequence reads were assembled together to form a 3X whole genome assembly allowing the discovery of over three million SNPs.
Cleaned reads from all libraries were assembled together using the RNA-seq de novo assembler Trinity [ 51] in the paired-end mode with the options ' min_kmer_cov = 2, −−dnorm_max_cov = 100'.
However, overlapping transcript alignments that have different introns in their region of overlap, due to a splicing variation, are found incompatible and cannot be assembled together, and hence occupy distinct maximal alignment assemblies.
In the second round, the PE and MP reads of the best length from the first round were assembled together with Velvet using several k-mer sizes, and the assembly with the maximum N50 was picked up as the final assembly.
