Search Results for "sequencing analysis"
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Showing 102 open source projects for "sequencing analysis"
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FastQC
A quality control analysis tool for high throughput sequencing data
FastQC is a quality control analysis tool designed to spot potential problems in high throughput sequencing datasets. Its goal is to provide a simple way by which to check the quality of raw sequence data coming from high throughput sequencing pipelines. It does this by running a modular set of analyses on one or more raw sequence files in fastq or bam format. It then produces a report summarizing the results, and highlighting any areas where the library may appear unusual. This should... -
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SuperCollider
Audio server, programming language, and IDE for sound synthesis
SuperCollider is a platform for audio synthesis and algorithmic composition, used by musicians, artists, and researchers working with sound. It is free and open source software available for Windows, macOS, and Linux. scsynth, a real-time audio server, forms the core of the platform. It features 400+ unit generators (“UGens”) for analysis, synthesis, and processing. Its granularity allows the fluid combination of many known and unknown audio techniques, moving between additive and subtractive... -
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miRge3
Comprehensive analysis of small RNA sequencing data
An update to Python package to perform comprehensive analysis of small RNA sequencing data, including miRNA annotation, A-to-I editing, novel miRNA detection, isomiR analysis, visualization through IGV, processing Unique Molecular Identifieres (UMI), tRF detection and producing interactive graphical output. miRge3.0 is developed in python v3.8 and is a recent update of our previous version miRge2.0. This build includes command line interface (CLI) and cross-platform Graphical User Interface... -
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popoolation
estimate natural variation and positive selection
PoPoolation is a pipeline for analysing pooled next generation sequencing data. Currently PoPoolation allows to calculate Tajima’s Pi, Watterson’s Theta and Tajima’s D with a sliding window approach for chromosomes or for set of genes. One of the main challenges in population genomics is to identify regions of intererest on a genome wide scale. We believe that PoPoolation will greatly aid this task by allowing a fast and user friendly analysis of NGS data from DNA pools. Documentation: https... -
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NGSEP
NGSEP (Next Generation Sequencing Experience Platform)
NGSEP is an integrated framework for analysis of short and long DNA high throughput sequencing reads. The current version provides functionalities for both de-novo and reference guided analysis of sequencing data, including genome assembly, read mapping, variants detection and genotyping and de-novo analysis of data generated from reduced representation protocols. NGSEP also provides modules for analysis of genomic variation databases (VCF files), including functional annotation, filtering... -
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BADASS is a software with a user-friendly graphical interface applied to the search and analysis of bacteriocin diversity in whole-metagenome shotgun sequencing data. The search for bacteriocin sequences is performed with tools such as BLAST or DIAMOND using the BAGEL4 database as a reference. The putative bacteriocin sequences identified are used to determine the abundance and richness of the three classes described so far. Abundance is calculated by comparing the reads identified...
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ViReMa
Viral Recombination Mapper
ViReMa (Viral Recombination Mapper) detects and reports recombination or fusion events in virus genomes using deep sequencing datasets. Feb 2014 - Our paper (Open Access) is available at Nucleic Acids Research: "Discovery of functional genomic motifs in viruses with ViReMa–a Virus Recombination Mapper–for analysis of next-generation sequencing data" http://nar.oxfordjournals.org/content/42/2/e11 This is an on-going project and updates will be regularly posted. Please get in touch... -
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MicroRNAs (miRNAs) are of significance in tuning and buffering gene expression. Despite abundant analysis tools have been developed in the last two decades, plant miRNA identification from next-generation sequencing (NGS) data remains challenging. Here present a user-friendly pure Java-based software package, SRICATs, which enable researchers to perform all steps of plant miRNA analysis based on convolutional neural network methods. SRICATs outperforms currently popular software tools...
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123VCF
An Intuitive and Efficient Tool for VCF file filtration
123VCF has been developed to make the filtration step of VCF files efficient and more importantly easy to understand. It can be used in the most important step of whole exome/genome sequencing data analysis in the research and also clinical settings. User manual: https://dl.adbioinformatics.net/123VCF/123VCF_Manual.ver2.pdf If you use 123VCF, please cite its paper: Eidi, M., Abdolalizadeh, S., Moeini, S. et al. 123VCF: an intuitive and efficient tool for filtering VCF files. BMC... -
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Seqs Extractor is a useful tool, and can reduce ambiguities in analyses which uses BLAST command ine, commonly in the next generation sequencing, Transcriptomics, Proteomics, etc and help extract BLASTed sequences and sequences that contains microsatellites. Seqs Extrator also turns the BLAST command line more friendly.
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MaChIAto Example Files
The example files of MaChIAto
MaChIAto (Microhomology-associated Chromosomal Integration/editing Analysis tools); a comprehensive analysis software that can precisely classify, deeply analyze, correctly align, and thoroughly review the targeted amplicon sequencing analysis data obtained by various CRISPR experiments, including template-free gene knock-out, short homology-based gene knock-in, and even a new-class CRISPR methodology, Prime Editing. In this repository, we provide the example files of MaChIAto. You can use... -
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MiModD
Mutation Identification in Model Organism Genomes using Desktop PCs
MiModD is a software package for genomic variant identification from next-generation sequencing (NGS) data with optimized usage of system resources and a user-friendly interface. For most model organism genomes it lets the user carry out a complete analysis from unaligned genomic NGS read data to an annotated list of variants on a regular Desktop PC within a few hours. Its user-interface is beginner-friendly and designed to encourage geneticists to analyze NGS data themselves without the help... -
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misc genomics tools
Various scripts used in sequencing, annotation and RNAseq analysis
This is a collection of various programs developed in the course of a genomics project, involving the Pseudomonas strain NCIMB10586 These include * identifying and correcting errors in an (eg) pacbio genome sequence using illumina reads * prokaryotic sequence/genome annotation * RNAseq analysis - normalisation and collation of multiple samples as a group * RNAseq visualisation All scripts are provided on a 'best efforts' basis, however due to various system changes I do not guarantee... -
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MutaNET
NGS Pipeline and Automated Mutation Analysis
MutaNET comes with a next generation sequencing (NGS) pipeline that calls mutations based on paired-end NGS reads, an automated mutation analysis tool and various file converters and mergers. The mutation analysis feature considers the coding region, protein domains, regulation and transcription factor binding site information, and can be used to analyse the potential impact of mutations on antibiotic resistance. -
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RESTAMP
Microbial division rate and death rate estimates.
RESTAMP - Rate Estimates By Sequence Tag Analysis of Microbial Populations, is an analytical framework for estimating microbial division rates and death rates. It consists of Matlab based software for producing founder population size values from next-generation sequencing data. It also includes scripts that implements the equations that determine the rates from CFU and founder population size values. -
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MToolBox
A bioinformatics pipeline to analyze mtDNA from NGS data
MToolBox is a highly automated bioinformatics pipeline to reconstruct and analyze human mitochondrial DNA from high throughput sequencing data. MToolBox includes an updated computational strategy to assemble mitochondrial genomes from Whole Exome and/or Genome Sequencing (PMID: 22669646) and an improved fragment-classify tool (PMID:22139932) for haplogroup assignment, functional and prioritization analysis of mitochondrial variants. MToolBox provides pathogenicity scores, profiles of genome... -
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... biopsy from cancers, quantitative transcriptome analysis to estimate accurate expression levels of genes or transcripts, and even single-cell sequencing of large cell populations. Operating system: Linux Programming language: C++ License: Non-Commercial Research Use Only
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TARGT pipeline
Targeted Analysis of sequence Reads for GenoTyping of HLA/MHC genes
The 'TARGT' pipeline for Targeted Analysis of sequencing Reads for GenoTyping can be used for genotyping of MHC/HLA genes (or other genomic regions) from ancient and modern shotgun sequence data with moderate to low sequence coverage. The pipeline consists of a main bash script that calls the different steps of the pipeline and can either be called directly or submitted to a cluster queue system, as well as additional sub-scripts and files, that are required to perform the different steps... -
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TaBS-Pipe
Targeted Bisulfite Sequencing Data Analysis Pipeline v1.0.2
A pipeline to analyze the data obtained from targeted bisulfite sequencing through the ion-torrent platform. TaBSAP is a pipeline to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step and enables a researcher to analyze the methylation levels of their samples straight away. It's main features are: -Bisulfite mapping and methylation calling in one single step -Supports single-end read alignments -Alignment seed length, number... -
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MIRA - Sequence assembler and sequence mapping for whole genome shotgun and EST / RNASeq sequencing data. Can use Sanger, 454, Illumina and IonTorrent data. PacBio: CCS and error corrected data usable, uncorrected not yet.
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NanoR
R package built to analyze and compare Nanopore data
NanoR is a package for the statistical language and environment R, tested on Unix, MacOSX and Windows, that allows user-friendly analysis and comparison of 1D MinION and GridION X5 sequencing data within acceptable time frames. -
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PhageTerm
Determining Bacteriophage Termini and Packaging using NGS data.
NEW VERSION (PhageTermVirome) AVAILABLE AT : (To access the lightest version) https://gitlab.pasteur.fr/vlegrand/ptv/-/releases This new version is now compatible with PYTHON3 and now allows the analysis of multiple phage genomes/contigs (multifasta) in a single analysis. However, like before, you can still perform the analysis on a single phage genome/contig. Description : PhageTerm and PhageTermVirome are a theoretical and statistical framework to analyze DNA termini and phage... -
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NanoGLADIATOR
Real-time detection of copy number alterations from nanopore data.
Nano-GLADIATOR is a novel software tool that allows to analyze WGS data generated during a MinION or GridION X5 run for the detection of copy number alterations (CNAs). Nano-GLADIATOR (Nanopore Genomic aLterations AnD allelIc frAcTiOn pRedictor) is capable to perform CNVs/CNAs detection and allelic fraction prediction during the sequencing run ("On-line" mode for real time molecular karyotyping) and once the experiment is completed ("Off-line" mode, for parallel analysis of multiple samples... -
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CSBB-v3.0
CSBB - Computational Suite for Bioinformaticians and Biologists
CSBB is a command line-based bioinformatics suite to analyze biological data acquired through varied avenues of biological experiments. CSBB is implemented in Perl, while it also leverages the use of R, java, python and ruby in background for specific modules. Major focus of CSBB is to allow users from biology and bioinformatics community, to get benefited by performing down-stream analysis tasks while eliminating the need to write programming code. CSBB is currently available on Linux, UNIX... -
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BisSNP
Bisulfite-seq/NOMe-seq SNPs & cytosine methylation caller
Now in Github: https://github.com/dnaase/Bis-tools/tree/master/Bis-SNP BisSNP is a package based on the Genome Analysis Toolkit (GATK) map-reduce framework for genotyping in bisulfite treated massively parallel sequencing (Bisulfite-seq, NOMe-seq and RRBS) on Illumina platform. It uses bayesian inference with either manually specified or automatically estimated methylation probabilities of different cytosine context(not only CpG, CHH, CHG in Bisulfite-seq, but also GCH et.al. in other...