TagCleaner

TagCleaner removes WTA and MID tag sequences from primer-amplified metagenomic sequencing reads to improve the quality of data for downstream analyses such as taxonomic profiling and functional annotation.

Key Features:

• Automatic tag detection and removal: Identifies known and unknown tag sequences (including WTA and MID tags) and removes them from reads while accommodating insertions and deletions.
• Handling ambiguities: Accounts for ambiguous bases in primer sequences and for unavailable or incorrectly reported tag sequences during detection and trimming.
• Data quality enhancement: Filters trimmed reads to remove duplicates, short reads, and reads with high rates of ambiguous bases, and splits artificial concatenated sequences arising from fragment-to-fragment concatenations.
• Customizable parameters: Allows modification of filter parameters to adjust trimming and filtering thresholds.

Scientific Applications:

• Taxonomic profiling: Produces cleaned reads suitable for accurate taxonomic assignment from metagenomic datasets.
• Functional annotation: Improves sequence quality for reliable gene and function identification in metagenomes.
• Comparative metagenomics: Enables reproducible comparisons across samples by removing amplification- and tag-derived artifacts.

Methodology:

Automatic identification of tag sequences, removal accommodating insertions and deletions, followed by filters that trim reads, remove duplicates and short/ambiguous reads, and split artificial concatenated sequences.