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.
Manages base call (BCL) conversion to FASTQ and demultiplexing. BCL2FASTQ’s sample demultiplexer allows users to: generate statistics, regenerate analysis plots for each multiplexed sample, copy raw matrix, phase file and update sample sheet. Furthermore, this program includes features to mask multiple adapter sequences per read with a configurable stringency of the adapter and has standard Illumina adapter sequences.
Allows users to process biological sequencing data. ea-utils works with pipeline based on Illumina and can run with other FASTQs. It offers several functions such as scanning a sequence file for adapters to determine a set of clipping parameters and perform clipping. It can demultiplex FASTQ files and can check if the reads are in-sync during the demultiplexing.
Enables users to find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. Cutadapt assists users in finding the adapter or primer sequences in an error-tolerant way. It can also modify and filter reads in various ways. Moreover, this program can work with paired-end reads and even colorspace data.
Assists users in manipulating high-throughput sequencing (HTS) data and formats. Picard is a Java toolkit that provides a set of command line scripts. It comprises Java-based utilities that manipulate SAM files, and a Java API for creating new programs that reads and writes SAM files. Both SAM text format and SAM binary (BAM) format are supported. It also works with next generation sequencing (NGS).
Preprocesses high-throughput sequencing data efficiently. Flexbar demultiplexes barcoded runs and removes adapter sequences. Several adapter removal presets for Illumina libraries are included. Flexbar computes exact overlap alignments using Single Instruction Multiple Data (SIMD) and multicore parallelism. Moreover, trimming and filtering features are provided: filter reads with uncalled bases, trim bases on left or right end, trim based on quality values, trim homopolymers at read ends, trim reads to certain length from right, and filter short sequencing reads. This tool increases read mapping rates and improves genome as well as transcriptome assemblies. Unique molecular identifiers can be extracted in a flexible way. The performance of the software was evaluated by adapter trimming
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.
Allows extraction and labelling of the sequences to be mapped in downstream pipelines, from next-generation sequencing (NGS) data. TagDust performs all steps required to go from raw to mappable sequences and therefore simplifies processing pipelines. The software, using hidden Markov models (HMMs), can work on datasets with a broad range of sequencing error rates. It enables users to define several read architectures and to use the same pipeline for the preprocessing of diverse data types.