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Table 1 Results of mapping, trimming and assembly of sequencing reads from three C. cayetanensis strains

From: A hybrid reference-guided de novo assembly approach for generating Cyclospora mitochondrion genomes

Attribute C. cayetanensis assemblies
C5 C8 C10
Total reads (metagenomic) 34 × 106 33 × 106 7.3 × 106
Source-reads (untrimmed)1 298,2141a (0.87%) 205,2671a (0.62%) 38,2061b (0.52%)
Source-reads (trimmed)1 298,214 205,265 38,206
Average read length (bp) 245 247 237
Reads used in the assembly 294,688 203,066 37,850
Reads mapped back2 298,144 (99.98%) 205,226 (99.98%) 38,195 (99.97%)
Genome coverage3,4 > 11,000 × > 8000 × > 1400 ×
  1. 1 Source-reads for each sample were obtained by mapping total metagenomic reads on to the KP231180 reference genome; 1a for either of C5 and C8, metagenomic reads from a 300 × 2 cycles paired-end and a 600 cycles single-end runs from a single library prep were pooled before mapping; 1b for C10, reads from a single 300 × 2 paired end run were used for mapping
  2. 2 Source-reads from each sample were mapped back to the reference genome and corresponding assembly. The same percentage was observed in either instance for each sample
  3. 3 Genome coverage (assuming all reads are from single-end runs) was based on the TechNote from Illumina available at https://www.illumina.com/documents/products/…/technote_coverage_calculation.pdf
  4. 4 For each sample, a mitochondrion assembly comprising of a single 6274 bp long contig was generated following the workflow described in Fig. 1. This was used to calculate the coverage