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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 origin, a process referred to as demultiplexing.

Source text:
(Renaudet al., 2015) deML: robust demultiplexing of Illumina sequences using a likelihood-based approach. Bioinformatics.

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Offers a platform for population-level analyses. dDocent is an open-source software dedicated to individually barcoded restriction-site associated DNA sequencing (RADseq) data processing. The application employs data reduction techniques and interact with other programs to propose features such as de novo assembly of RAD loci, single nucleotides polymorphisms (SNPs) and indel calling as well as quality trimming or baseline data filtering.
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Finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. Cutadapt helps with these trimming tasks by finding the adapter or primer sequences in an error-tolerant way. It can also modify and filter reads in various ways. Adapter sequences can contain IUPAC wildcard characters. Also, paired-end reads and even colorspace data is supported. If you want, you can also just demultiplex your input data, without removing adapter sequences at all.
Builds genetic maps and conducts population genomics and phylogeography. Stacks is a software system developed to work with restriction enzyme-based data, such as RAD-seq. The software produces core population genomic summary statistics and single nucleotide polymorphism (SNP)-by-SNP statistical tests. It aims to be a key resource to empower researchers to efficiently perform ecological and evolutionary genomic studies in model organisms and particularly in organisms with minimal or no genomic resources.
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 containing a set of outer codewords, expands them according to an inner codebook and imprints them with a watermark sequence to produce a set of barcodes, which are saved to an output file. watermarkDecoder decodes sequencing reads with embedded watermark barcodes.
RADIS / analysis of RAD-seq data for InterSpecific phylogeny
Automates and standardizes the analyses of RAD-seq data for phylogenetic inference. Users of RADIS can let their raw Illumina data be processed up to phylogenetic tree inference, or stop (and restart) the process at some point. Different values for key parameters can be explored in a single analysis (e.g. loci building, sample/loci selection), making possible a thorough exploration of data. RADIS relies on Stacks for demultiplexing of data, removing PCR duplicates and building individual and catalog loci. Scripts have been specifically written for trimming of reads and loci/sample selection. Finally, RAxML is used for phylogenetic inferences, though other software may be utilised.
MAGERI / Molecular tAgged GEnome Re-sequencing pIpeline
Allows to obtain high-fidelity mutation profiles and call ultra-rare variants by handling caveats of Unique Molecular Identifier (UMI)-based analysis. MAGERI accounts for polymerase chain reaction (PCR) errors by using a variant quality scoring model. It can handle reads with high error load, indels and random offsets. The tool was able to detect circulating tumor DNA (ctDNA) in peripheral blood of cancer patients. It allows easy and efficient processing of high-throughput sequencing data generated.
GBS-SNP-CROP / GBS SNP Calling Reference Optional Pipeline
Discovers SNP and characterizes plant germplasm. GBS-SNP-CROP adopts a clustering strategy to build a population-tailored “Mock Reference” from the same GBS data used for downstream SNP calling and genotyping. It may be used to augment the results of alternative analyses, whether or not a reference is available. The tool may complement other reference-based pipelines by extracting more information per sequencing dollar spent. GBS-SNPCROP may be useful even in this case, able to detect large numbers of additional high-quality SNPs missed by the tag-based and read length-restricted approach of TASSEL-GBS.
A Genotyping-by-sequencing (GBS) bioinformatics pipeline designed to provide highly accurate genotyping. Fast-GBS is capable of handling data from different sequencing platforms and can detect different kinds of variants (Single Nucleotide Polymorphisms (SNPs), Multiple Nucleotide Polymorphisms (MNPs), and Indels). This pipeline was benchmarked based upon a large-scale, species-wide analysis of soybean, barley and potato. It is easy to use with various species, in different contexts, and provides an analysis platform that can be run with different types of sequencing data and modest computational resources.
A comprehensive tool for analyzing next-generation sequencing data. AdapterRemoval is able to pre-process both single and paired-end data. The program locates and removes adapter residues from the reads, it is able to combine paired reads if they overlap, and it can optionally trim low-quality nucleotides. Furthermore, it can look for adapter sequence in both the 5' and 3' ends of the reads. This is a flexible tool that can be tuned to accommodate different experimental settings and sequencing platforms producing FASTQ files. AdapterRemoval is shown to be good at trimming adapters from both single-end and paired-end data.
RELACS / Restriction Enzyme-based Labeling of Chromatin in Situ
Allows generation of ChIP-seq libraries. RELACS is a high-throughput ChIP-seq method based on the enzymatic cutting and barcoding of chromatin inside intact nuclei. The software can be used for a broad spectrum of epitopes and cell types. It can also be applied to fixed samples, allowing profiling of transcription factors and co-factors easily lost by native ChIP approaches. RELACS was validated using a well-studied human cell line (HepG2) for which many external references are available.
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 compares the provided barcodes with each read and separates the read into its appropriate barcode file, after stripping the barcode from the read (and also stripping the quality values of the barcode bases). If a read does not have a recognized barcode, then it is put into the unknown file.
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