rgestlibcomp

rgestlibcomp estimates library complexity from sequence data to quantify the diversity of unique sequences in next-generation DNA sequencing workflows.

Key Features:

• Read Sorting: Sorts reads by their first N bases (default N=5) to group similar sequences for comparison.
• Duplicate Detection: Identifies duplicate reads among those with identical starting bases by requiring exact matches without gaps and an overall mismatch rate ≤ the default MAX_DIFF_RATE of 0.03.
• Parameter Customization: Allows adjustment of N (number of bases for sorting) and MAX_DIFF_RATE to suit experimental requirements.

Scientific Applications:

• Sequencing depth optimization: Estimates library complexity to inform necessary sequencing depth for a given sample.
• Coverage assessment for rare variants: Helps determine whether sequencing provides sufficient coverage to detect rare variants.
• Data quality evaluation: Quantifies the proportion of unique sequences to assess library diversity and potential duplication biases.
• Experimental design and interpretation: Provides complexity estimates that inform experimental design choices and downstream data interpretation.

Methodology:

Reads are organized by their initial sequence segment (first N bases), compared within these groups to identify duplicates based on exact-match/no-gap criteria and a mismatch-rate threshold (MAX_DIFF_RATE), and the proportion of unique sequences is quantified to estimate library complexity.