Adapter removal software tools | High-throughput sequencing data analysis
Contaminant oligonucleotide sequences such as primers and adapters can occur in both ends of next-generation sequencing (NGS) reads. These adapter sequences have to be removed as they can hinder correct mapping of the reads and influence SNP calling and other downstream analyses.
Assists in automating quality, adapter trimming and quality control (QC). Trim Galore! is a wrapper script that provides functionalities to remove biased methylation positions for reduced representation bisulfite sequencing (RRBS) sequence files (for directional, non-directional (or paired-end) sequencing). It can remove sequences if they become too short during the trimming process.
Performs a variety of trimming tasks for Illumina paired-end and single ended data. Trimmomatic is a pair-aware preprocessing tool optimized for Illumina next-generation sequencing (NGS) data. The software includes several processing steps for read trimming and filtering. It uses a pipeline-based architecture allowing individual ‘steps’ (adapter removal, quality filtering, etc.) to be applied to each read/read pair, in the order specified by user.
Gives access to many free software tools for sequence analysis. EMBOSS aims to serve the molecular biology community. It permits the creation and the release of software in an open source spirit. This tool is useful for sequence analysis into a seamless whole. It is free of charge and is available in open source.
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.
A tool for automated alignment trimming, which is especially suited for large-scale phylogenetic analyses. trimAl can consider several parameters, alone or in multiple combinations, for selecting the most reliable positions in the alignment. These include the proportion of sequences with a gap, the level of amino acid similarity and, if several alignments for the same set of sequences are provided, the level of consistency across different alignments. Moreover, trimAl can automatically select the parameters to be used in each specific alignment so that the signal-to-noise ratio is optimized.
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.