Comparative assessment of variant detection based on <i>Prunus persica</i> reads aligned on the reference peach genome.

<p>Several read trimming method/threshold combinations are tested. The Average Percentage of Minor Allele Call (APOMAC) or of Non-reference Allele Call (APONAC) are reported, together with the total number of high-confidence SNPs.</p

Number of covered nucleotides in the <i>Prunus persica</i> genome (total size: 227M bases) above minimum coverage thresholds.

<p>The analysis was performed on untrimmed reads and after trimming with 9 tools at Q=20 (for ConDeTri, default parameters HQ=25 and LQ=10 were used).</p

Computational requirements necessary for full <i>Prunus persica</i> genome assembly (RAM peak and time) for different combinations of read trimming tools and thresholds.

<p>Computational requirements necessary for full <i>Prunus persica</i> genome assembly (RAM peak and time) for different combinations of read trimming tools and thresholds.</p

Fraction of reads mapped vs. number of reads in the quality trimmed <i>Homo sapiens</i> RNA-Seq dataset.

<p>Each symbol corresponds to a quality threshold. Peak Q parameters for each tool are reported.</p

Hpa01S_lib

Hpa01S_li

Hpy01S_lib

Hpy01S_li

Barplots indicating the performance of nine read trimming tools at different quality thresholds on a <i>Homo sapiens</i> RNA-Seq dataset.

<p>For ConDeTri, two basic parameters are necessary, and combinations of both are reported (which explains the non-monotonic appearance of the barplots). Red bars indicate the percentage of reads aligning in the trimmed dataset. Blue bars indicate the number of reads surviving trimming.</p

Hpa1S_lib

Hpa1S_li

Hpy01N_lib

Hpy01N_li

Hpy1S_lib

Hpy1S_li