A xeb app which trims reference sequences based on user-selected primer pairs and returns an assessment of the primer specificity by taxa. TaxMan also provides graphical analysis of the taxa that are selected for or against with the selected primer sets. It can be used to analyze the taxonomic coverage of the trimmed sequences (amplicons), and the original reference database sequences.
Removes gene-specific primer sequences from SAM/BAM alignments of polymerase chain reaction (PCR) amplicons by soft-clipping. BAMClipper is an open-source, fast and effective tool to remove primers from mapped alignments of amplicon sequencing reads. This method is efficient in computation and maintained equally high primer removal effectiveness and maintained the same high level of primer removal effectiveness as conventional trimming approach.
Allows to trim primer sequences from amplicon based next generation sequencing (NGS) reads. cutPrimers simultaneously searches the primer sequences in the pairs of the reads and enables to remove the primer sequences from the reads owing to the use of multithreading. During processing of the reads, the program can save error statistics in the primers. Moreover, it can detect primer dimers that may form during amplification.
Produces improved results of variable length amplicons from HTAS. AMPtk is a bioinformatic pipeline developed to specifically address the quality issues identified by using spike-in mock communities. It analyzes variable length amplicon studies such as the fungal ITS1 or ITS2 molecular barcodes. This method provides the scientific community with a necessary tool to study fungal community diversity.
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