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Demultiplexing software tools | High-throughput sequencing data analysis

Pooling multiple samples increases the efficiency and lowers the cost of DNA sequencing. One approach to multiplexing is to use short DNA indices to uniquely identify each sample. After sequencing, reads must be assigned in silico to the sample of…
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Flexbar
Desktop

Flexbar

Allows barcode and adapter detection. Flexbar calculates full overlap…

Allows barcode and adapter detection. Flexbar calculates full overlap alignments using Single Instruction Multiple Data (SIMD) and multicore parallelism. It allows to filter reads with uncalled…

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Barcas
Desktop

Barcas

Permits analysis of multiplexed barcode-seq data. Barcas maps sequenced reads…

Permits analysis of multiplexed barcode-seq data. Barcas maps sequenced reads based on the trie data structure for fast and efficient imperfect matching. It constructs a trie data structure from the…

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Kraken
Desktop

Kraken

A set of tools for quality control and analysis of high-throughput sequence…

A set of tools for quality control and analysis of high-throughput sequence data.

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expandAndWaterm…
Desktop

expandAndWatermark/watermarkDecoder

Software tools for constructing watermark barcode sets and demultiplexing…

Software tools for constructing watermark barcode sets and demultiplexing barcoded reads, together with example sets of barcodes and synthetic barcoded reads. expandAndWatermark takes an input file…

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ClonoCalc
Desktop

ClonoCalc

Prepares the raw data for downstream analyses. ClonoCalc combines a…

Prepares the raw data for downstream analyses. ClonoCalc combines a demultiplexer for barcode splitting and employs MiXCR for paired-end read merging and the extraction of human and animal T cell…

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AXE
Desktop

AXE

Allows demultiplexing 5’-indexed reads. Axe matches the prefix of a sequence…

Allows demultiplexing 5’-indexed reads. Axe matches the prefix of a sequence read against a pre-computed trie of index sequences. It starts by calculating all sequences within a given hamming…

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Bayexer
Desktop

Bayexer

A Bayesian demultiplexing algorithm for Illumina sequencers. Bayexer uses the…

A Bayesian demultiplexing algorithm for Illumina sequencers. Bayexer uses the information extracted directly from the contaminant sequences of the targeting reads as the training dataset for a naïve…

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deML
Desktop

deML

A maximum likelihood algorithm that demultiplexes Illumina sequences. deML…

A maximum likelihood algorithm that demultiplexes Illumina sequences. deML computes the likelihood of an observed index sequence being derived from a specified sample. A quality score which reflects…

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TagGD
Desktop

TagGD DNA-based Tag Generator and Demultiplexor

A fully-customisable, fast and accurate software package that can generate…

A fully-customisable, fast and accurate software package that can generate thousands of barcodes satisfying user-defined constraints and can guarantee full demultiplexing accuracy. The barcodes are…

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Reaper
Desktop

Reaper

A program for demultiplexing, trimming and filtering short read sequencing…

A program for demultiplexing, trimming and filtering short read sequencing data. Reaper is intended to be suitable for dealing with a wide range of sequencing protocols, and will be updated to…

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sabre
Desktop

sabre

A barcode demultiplexing and trimming tool for FastQ files. sabre will…

A barcode demultiplexing and trimming tool for FastQ files. sabre will demultiplex barcoded reads into separate files. It will work on both single-end and paired-end data in fastq format. It simply…

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ea-utils
Desktop

ea-utils

Allows users to process biological sequencing data. ea-utils works with…

Allows users to process biological sequencing data. ea-utils works with pipeline based on Illumina and can run with other FASTQs.

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