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. Author manuscript; available in PMC: 2022 Nov 28.
Published in final edited form as: Methods Enzymol. 2018 Feb 21;601:111–144. doi: 10.1016/bs.mie.2017.11.028

Table 2.

The Number of Sequencing Reads Retained Following Each Processing Step in the Analysis

Processing Step Counts Percent
Retained
fastq 1134957 100
Trimmed 1101132 97.01971088
Geneious 1100535 96.96710977
Hi-FiBR Geneious (No Processing Window Correction) 1100535 96.96710977
Hi-FiBR Geneious (8 bp Processing Window Correction) 1100535 96.96710977
CLC 1099030 96.83450562
Hi-FiBR CLC (No Processing Window Correction) 1054561 92.91638362
Hi-FiBR CLC (8 bp Processing Window Correction) 1054561 92.91638362
Bowtie2 1070588 94.3285076
Hi-FiBR Bowtie2 (No Processing Window Correction) 1070588 94.3285076
Hi-FiBR Bowtie2 (8 bp Processing Window Correction) 1070588 94.3285076
BWA 1100458 96.96032537
Hi-FiBR BWA (No Processing Window Correction) 1097364 96.68771592
Hi-FiBR BWA (8 bp Processing Window Correction) 1097364 96.68771592

About 3% of reads are lost to the trimming step, and the remaining lost are due to the alignment tools. The order of most reads retained from highest to lowest is Geneious (~97%), BWA (~96.7%), Bowtie2 (~94%), and CLC (~93%). No difference occurs from the size of the processing window adjustment.