Abstract
We describe a rapid algorithm for demultiplexing DNA sequence reads with in-read indices. Axe selects the optimal index present in a sequence read, even in the presence of sequencing errors. The algorithm is able to handle combinatorial indexing, indices of differing length and several mismatches per index sequence. Axe is implemented in C, and is used as a command-line program on Unix-like systems. Axe is available online at https://github.com/kdmurray91/axe, and is available in Debian/Ubuntu distributions of GNU/Linux as the package axe-demultiplexer. Supplementary data are available at Bioinformatics online.
Highlights
The incredible yield of modern DNA sequencing technologies has enabled the multiplexing of DNA samples into a single sequencing unit
2 Methods 2.1 Implementation Axe matches the prefix of a sequence read against a pre-computed trie of index sequences
Axe first calculates all sequences within a given hamming distance of each index sequence
Summary
The incredible yield of modern DNA sequencing technologies has enabled the multiplexing of DNA samples into a single sequencing unit. Multiplexing is achieved by the addition of short sequences (indices) to each molecule to be sequenced. When sequenced, these index sequences uniquely identify the sample to which a sequence read belongs. Many commercial protocols use platform specific features to add these DNA indices such that sequencing platforms can automatically demultiplex these samples. Many custom sequencing protocols, including GBS [2], add indices which end users must themselves demultiplex. Many sequencing read demultiplexers have been published Both Flexbar [1] and the Fastxtoolkit’s fastx_barcode_splitter.pl [3] accept single- and paired-end reads, they cannot demultiplex combinatorial indices.
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