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

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

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 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 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 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

ISSN: 1757-4749