Table 1.
Read pre-processing strategies used in this study.
| Pre-processing strategy∗ | Quality trimming∗∗ | Merging of overlapped pairs∗∗∗ | PCR de-duplication∗∗∗∗ |
|---|---|---|---|
| Lax | Lead:Q20, Trail:Q15, Wlen:10,Q15 | No | No |
| Medium | Lead:Q25, Trail:Q20, Wlen:15,Q20 | No | No |
| Hard | Lead:Q25, Trail:Q25, Wlen:20,Q25 | No | No |
| Lax + Ovl | Lead:Q20, Trail:Q15, Wlen:10,Q15 | Min Ovl 15 bp | No |
| Medium + Ovl | Lead:Q25, Trail:Q20, Wlen:15,Q20 | Min Ovl 15 bp | No |
| Hard + Ovl | Lead:Q25, Trail:Q25, Wlen:20,Q25 | Min Ovl 15 bp | No |
| Lax + PCR | Lead:Q20, Trail:Q15, Wlen:10,Q15 | No | MDR = 0.03 |
| Medium + PCR | Lead:Q25, Trail:Q20, Wlen:15,Q20 | No | MDR = 0.03 |
| Hard + PCR | Lead:Q25, Trail:Q25, Wlen:20,Q25 | No | MDR = 0.03 |
From left to right, columns contain:
∗Description of the strategy, as described in main text and figures.
∗∗Trimmomatic parameters for quality trimming. Q, quality score cut-off; Wlen, length of the window for sliding window operations.
∗∗∗Pear parameters for read merging. Min Ovl, minimum overlap required for merging of read pairs.
∗∗∗∗MarkDuplicates parameters for PCR de-duplication. MDR (MAX DIFF RATE), overall mismatch rate for non-duplicated reads.