In this case, it was possible to assemble more reads into contigs with Illumina than with 454, leading to much higher maximum contig length and N50 values.
The other assemblies had longer and fewer contigs, which had higher average alignment length, with the meta-assembly showing the best performance (i.e. fewest number of contigs with highest average aligned contig length (Table 2).
Higher N50 contig lengths were obtained in this experiment (∼1 Mbp in bacteria, ∼100 Kbp in human) than in the previous simulations with mixed length reads.
Since all assemblies obtained with the latter program resulted in significantly higher N50/N80 contig lengths and less gaps when compared to the Sanger references, sequence assembly by Newbler was skipped for further analysis of the data.
Flag leaves showed highest contig number (43,467) but lowest contig length (688 bp).
The two assemblies that included PacBio data (BCM and CBCB) had the highest and second-highest contig NG50 lengths among all competitive bird assemblies (Additional file 2: Figure S1), suggesting that inclusion of PacBio data may be particularly useful in this regard.
For the second trimmed data set, although the largest contig length was highest for k = 41 (10 616 bp), N50 length of 730 bp and average contig length of 453 bp were better for k = 47.
The preliminary set of contigs was searched with the eleven wheat paralogs using BLASTn to eliminate duplicates and to select contigs with the longest contig length and highest sequence similarity.
We identified 236 contigs that were highly variable (in the 99th percentile for highest ratio of variants per contig length) and, as expected of quickly evolving genes, few of these (19%) had homology hits in the BlastX searches, but 98% of them had predicted open reading frames (ORF) larger than 30 bp.
The de novo assembly had high contiguity, with a mean contig length of 1,102 bases.
