Sentence examples for overall assembly size from inspiring English sources

Many metrics such as singleton and contig count, coverage, N50, and overall assembly size were simply repurposed from whole-genome assembly evaluation.

Fosmid coverage was seen to vary between assemblies, particularly in snake, but was not correlated with genome assembly size (Additional file 2: Figure S8), reinforcing the notion that overall assembly size is not necessarily a good predictor of assembly quality.

Using custom settings with the Celera Assembler produced assemblies with the smallest overall assembly size and highest average ortholog hit ratio, a measure of assembly quality (Table 1, see Annotation).

The control unamplified TruSeq library had an overall assembly size of 60 Mb, total number of contigs was 43,848, contig N50 was 1271 bp, largest contig was 1.3 Mb and 95%% of reads could be mapped back to the assembly.

Paired-reads passing these quality filters were used to estimate the genome size for each strain using the program khmerfreq [ 34] using kmer = 17 and then assembled using SOAPdenovo software [ 34] with different kmer lengths (57 64), with the final assembly selected based on overall assembly size, number of contigs and contig size.

The overall assembly sizes of CAP3, CLC and Newbler 2.3 are comparable to each other (between 14.4 and 16.7 Mb), as are the assembly sizes of MIRA, Newbler 2.5 and SeqMan (between 20.0 and 21.3 Mb).

DOI: http://dx.doi.org/10.7554/eLife.04775.006 There was a trade-off in the assemblies between N50 and overall assembly lengths, as a function of kmer size.

Although many contigs fall in the 100 – 400 kb range, the contribution of the ranges to the overall assembly length was observed to be roughly uniform across all size ranges.

a d, Tukey boxplots of total assembly size, maximum and average contig lengths, and gene counts for single and co-assemblies (sample sizes in Supplementary Table 1).

In total, 406 and 240 co-assemblies were created by combining 2 and 3 visits, respectively (Supplementary Table 6), and the assembly sizes were on average 86% larger than single assemblies: the median assembly size increased from 84.8 Mb to 158.4 Mb, and the median of the maximum contig size in each assembly increased from 152 kilobases (kb) to 167 kb (Fig. 4a c).

The total assembly size was 2.30 Gb, with the longest scaffold 41.92 Mb in length.