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Trimmomatic
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Performs a variety of trimming tasks for Illumina paired-end and single ended data. Trimmomatic is a flexible, 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.
AlienTrimmer
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Detects and removes multiple alien sequences in both ends of sequence reads. Based on the decomposition of specified alien nucleotide sequences into k-mers, AlienTrimmer is able to determine whether such alien k-mers are occurring in one or in both read ends by using a simple polynomial algorithm. Therefore, AlienTrimmer can process typical HTS single- or paired-end files with millions of reads in several minutes with very low computer resources.
skewer
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Implements a dynamic programming algorithm dedicated to the task of adapter trimming. Skewer is specially designed for processing illumina paired-end sequences. Experiments on simulated data, real data of small RNA sequencing, paired-end RNA sequencing, and Nextera LMP sequencing showed that Skewer outperforms all other similar tools that have the same utility. Further, Skewer is considerably faster than other tools that have comparative accuracies; namely, one times faster for single-end sequencing, more than 12 times faster for paired-end sequencing, and 49% faster for LMP sequencing.
PEAT / Paired-End Adapter Trimmer
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Provides an adapter-trimmer algorithm for paired-end sequencing. PEAT utilizes a two-stage algorithm to find the proper trimming positions in linear time without loss of sensitivity and specificity. This software exploits the self-reverse complementary nature of adapter-appended read pairs. No a priori adapter sequence is required to run this tool. It can be efficiently incorporated in a routine paired-end sequencing pipeline.
Seqpurge
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A highly-sensitive adapter trimmer that uses a probabilistic approach to detect the overlap between forward and reverse reads of Illumina sequencing data. SeqPurge can detect very short adapter sequences, even if only one base long. Compared to other adapter trimmers specifically designed for paired-end data, SeqPurge achieves a higher sensitivity. The number of remaining adapter bases after trimming is reduced by up to 90 %, depending on the compared tool. In simulations with different error rates, SeqPurge is also the most error-tolerant adapter trimmer in the comparison.
dDocent
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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.
NGS-QC Generator / Next Generation Sequencing Quality Control generator
Assists users to evaluate the quality of ChIP-seq. The NGS-QC database hosts quality scores for over 28,000 datasets, covering a variety of ChIP-sequencing and related assays performed from about 8 species (Homo sapiens: 54%; Mus musculus: 34%; D. melanogaster: 6%). It contains an algorithm designed to: (i) infer a set of global QC indicators (QCis); or to (ii) provide local QCis to judge the robustness of cumulative read counts in a particular region.
cutadapt
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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.
Stacks
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.
MICRA / Microbial Identification and Characterization through Reads Analysis
Identifies and defines microbes via reads analysis. MICRA employs read mapping methods to make use of the increasing number of sequenced microbial genomes. The working consists in four parts: (1) pre-processing, (2) sequence identification, (3) identification of the closest reference genome and plasmids by the core part and (4) the post-analysis. This pipeline software is available as a download version and as a web interface.
BBMap
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Uses as a splice-aware aligner for short and long reads. BBMap is shown to be a fast and accurate aligner, capable of correctly handling an overall wider variety of references, reads, and mutations than others. It has particularly outstanding performance with deletions, especially long ones, that other aligners cannot handle at all. It can output many different statistics files, such as an empirical read quality histogram, insert-size distribution, and genome coverage, with or without generating a sam file.
Octopus-toolkit
Examines epigenomic and transcriptomic next generation sequencing (NGS) data. Octopus-toolkit can be used for antibody- or enzyme-mediated experiments and studies for the quantification of gene expression. It can accelerate the data mining of public epigenomic and transcriptomic NGS data for basic biomedical research. This tool provides a private and a public mode: one to process the user’s own data, and the other to analyze public NGS data by retrieving raw files from the GEO database.
TagDust
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.
CLC bio / CLC Genomics Workbench
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Allows to analyze, compare, and visualize next generation sequencing (NGS) data. CLC Genomics Workbench offers a complete and customizable solution for genomics, transcriptomics, epigenomics, and metagenomics. The software enables to generate custom workflows, which can combine quality control steps, adapter trimming, read mapping, variant detection, and multiple filtering and annotation steps into a pipeline.
trimAl
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.
ShortRead
A package for input, quality assessment, manipulation and output of high-throughput sequencing data. ShortRead extends Bioconductor with tools useful in the initial stages of short-read DNA sequence analysis. Main functionalities include data input, quality assessment, data transformation and access to downstream analysis opportunities. It is an important gateway to use of Bioconductor for processing high-throughput DNA sequence data. ShortRead data structures allow convenient manipulation of data, such as filtering reads based on sequence characteristics.
NGS-Trex / NGS TRanscriptome profile EXplorer
Allows user to upload raw sequences and obtain an accurate characterization of the transcriptome profile. NGS-Trex can assess differential expression at both gene and transcript level. It compares the expression profile of different samples. All comparisons are performed using a custom database which is mainly populated with several sources obtained from the NCBI. The tool allows user to discard ambiguously assigned reads or to assign those reads to all competing genes in the case of ambiguities.
SAMSA / Simple Analysis of Metatranscriptome Sequence Annotations
Analyzes and characterizes activity within a metatranscriptome. SAMSA has four phases: (1) the preprocessing phase trims and combines reads for input to the annotation phase; (2) the annotation phase provides an annotation for each read; (3) the aggregation phase aggregates organism and function information across all reads; and (4) the analysis phase provides visualizations and statistical analysis. It runs either in-house or in conjunction with Metagenome-RAST (MG-RAST) servers.
PHYLUCE
A package for phylogenomic analyses of data collected from conserved genomic loci using targeted enrichment. PHYLUCE allows the assembly of raw read data to contigs, the identification of ultra-conserved elements (UCE) contigs, parallel alignment generation, alignment trimming, and alignment data summary methods in preparation for analysis and alignment and SNP calling using UCE or other types of raw-read data. As it stands, the PHYLUCE package is useful for analyzing both data collected from UCE loci and also data collection from other types of loci for phylogenomic studies at the species, population, and individual levels.
Figaro
Identifies and removes the vector from raw DNA sequence data without prior knowledge of the vector sequence. Figaro is able to determine which DNA words are most likely associated with vector sequence by statistically modeling short oligonucleotide frequencies within a set of reads. This algorithm can be used to correctly identify the vector clipping points for sequences obtained from public databases. The code was implemented as a single streamlined module which can be easily integrated into a high-throughput computational pipeline. The code is distributed through the AMOS package.
ERNE / Extended Randomized Numerical alignEr
A short string alignment package whose goal is to provide an all-inclusive set of tools to handle short (NGS-like) reads. ERNE 2 (a.k.a. bw-erne) uses the Burrows Wheeler Transformation (BWT) to reduce memory requirements preserving its speed and accuray. ERNE 2 comprises ERNE-MAP (core alignment tool/algorithm), ERNE-BS5 (bisulfite treated reads aligner), ERNE-FILTER (quality trimming and contamination filtering), and parallel version of the aligners (ERNE-PMAP and ERNE-PBS5). The alignment core supports indels and one long gap.
ST Pipeline
Permits to process and analyze the raw files generated with the Spatial Transcriptomics (ST) method. ST Pipeline enables demultiplexing of spatially-resolved RNA-seq data and robust quality filtering and identification of unique molecules. It is highly customizable with numerous parameter settings. The tool is more robust, efficient and scales better to arrays with higher density. It filters data, aligns it to a genome, annotates it to a reference, demultiplexes by array coordinates and then aggregates by counts that are not duplicates using the Unique Molecular Identifiers.
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.
zUMIs
Processes raw reads to count tables for RNA-seq data using Unique Molecular Identifiers (UMIs). zUMIs is a pipeline applicable for most experimental designs of RNA-seq data, such as single-nuclei sequencing techniques. This method allows for down sampling of reads before summarizing UMIs per feature, which is recommended for cases of highly different read numbers per sample. zUMIs is flexible with respect to the length and sequences of the barcodes (BCs) and UMIs, making it compatible with a large number of protocols.
FASTX-Toolkit
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A collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. Next-Generation sequencing machines usually produce FASTA or FASTQ files, containing multiple short-reads sequences (possibly with quality information). The main processing of such FASTA/FASTQ files is mapping (aka aligning) the sequences to reference genomes or other databases using specialized programs. Example of such mapping programs are: Blat, SHRiMP, LastZ, MAQ and many many others.
Chipster
Consists of a collection of investigation approaches and displays software for microarray data. Chipster is useful for several types of high throughput data such as microarrays, proteomics and next generation sequencing (NGS). It can be employed to normalize most of the commonly used chip types and permits to utilize the remapped information. This tool is useful for RNA degradation, relative log expression (RLE), normalized unscaled standard error (NUSE) or quality control probe expression.
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