Assembly of such hybrid datasets results in contigs comprised of reads of varying length, which must be taken into account when calculating the number of reads per bin.
Nearly all of the contigs assembled de novo from unmapped reads that were identified as representing a non-vertebrate species were comprised of reads that originated from multiple libraries sequenced at separate facilities.
We only considered the small RNA loci that were expressed in all of the five genotypes and comprised of reads belonging to two or more length categories (19 31 nt) with a total read count of ≥5 in at least one of the genotypes.
In general, datasets with longer reads (e.g. 101 bp PE reads) resulted in a higher proportion of uniquely mapped reads than those comprised of shorter reads (e.g. 50 bp SE reads).
The raw sequencing data was comprised of 793 M reads with a read length of 75 bp which were generated for the single-end library, 1642 M reads with read length of 60 bp × 60 bp which were generated for the 2 Kb mate-paired library, and 1548 M reads with read length of 60 bp × 60 bp which were generated for the 5 Kb mate-paired library.
In our unigenes sequences, 22,723 contigs were comprised of 2-10 reads (minimum read range).
For comparison to the Table 1, we consider an example 114 kilobase contig of the population-sourced Anopheles gambiae genome assembly (Lawniczak et al., [ 26]) comprised of 984 reads containing 879 non-redundant reads with the largest of 12 haplotype blocks containing 481.
The read length distribution is comprised of all read lengths sampled.
In the case of the 1X102.5 pfu/mL sample, although 11/604,130 resulting reads map to the reference, covering 31% of the viral genome, de novo assembly of the reads produces a single contig comprised of 2 reads that covers only 4% of the viral genome (Table 1).
Furthermore, we have a higher probability of identifying SNPs when we compare contigs comprised of 100 reads than with those comprised of 2 sequence reads.
