For each of these two programs, we performed seven assemblies that can be divided into the following three categories: assembly of all four samples as a whole (designated as AFSFASSS), assembly of samples with the same phenotype (designated as AFSF and ASSS) and assembly of each of the four samples individually (designated as AF, SF, AS, and SS).
The proportion of C. trachomatis reads was sufficient for de novo assembly of samples CT-33 and CT-38, generating three and ten contigs respectively, whereas the proportion of reads mapping to C. trachomatis was suboptimal for de novo assembly of six samples (CT-34, CT-36, CT-37, CT-40, CT-41, CT-42), generating between 46 297 contigs.
To evaluate the performance of assembling all libraries at the initial stage and assembling each library separately and then merging them for each of the two assemblers, we performed three assemblies, AFSFASSS, AFSF + ASSS, AF + SF + AS + SS, representing the assembly of all samples, samples with the same phenotype, and individual samples at the initial stage, respectively.
By comparison, assemblies of samples at 1X10 pfu/mL and 1X10 pfu/mL yielded one contig of 9445 bp and two contigs of 4640 and 3566 bp, respectively.
In these experiments, successful assembly of mixed samples was not dependent on the abundance of repetitive sequences or on the GC content of the genomes (Table S2).
To simulate the assembly of mixed samples in a sequencing run, we used randomly fragmented subsets of four cyanophages genomes: P-SSM4, P-SSP7, P-SSM2, MED4 247, and MED4 259, comprising both myo- and podoviruses with sizes of approximately 50 kb to 252 kb (Table S2), and attempted to reassemble them using Newbler.
SAXS data were collected at beamline 12.3.1 of the Advanced Light Source, Lawrence Berkeley National Laboratory, at 12 keV on a MAR165 detector and used to analyze the solution architecture, conformation, and assembly of BARD1 samples.
While the delineation of these sampling buffers involved a number of simplifying assumptions, their purpose was only to facilitate the assembly of a sample of participants with some heterogeneity of exposure to the intervention.
The Stacks package [ 25] was then used to make a de-novo assembly of the sampled loci from each individual: 82,745 and 83,668 RAD-tags were retrieved for Families B and C respectively, covering 90,105 RAD-tags in total including 76,308 of these shared between the two families.
For the single k-mer assembler Trinity, merging assemblies of individual samples increased the number of mappable reads (Table 4) and the proportion of bases covered from full-length cDNA and public ESTs (Tables 6, 7), suggesting that the merging strategies broadened the coverage of the assemblies produced by Trinity.
Assemblies of individual samples were merged with both strands information using the accurate mode of cd-hit-est version 4.5.4 with the sequence identity threshold at 100% and a word size of 8 [ 15].
