Search Results for "amplicon"
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Showing 21 open source projects for "amplicon"
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Amplicon_Sequencing_Worfklow
Analyzing amplicon data from sequences to stats
This is a collection of scripts and instructions on how to analyzing amplicon sequence data (i.e., 16S, ITS2, & other marker genes). I created this workflow to create a consistent set of methods for analyzing amplicon sequence data, from when you first receive the sequence data to statistical analyses & data visualization. All you need is to have the latest version of R installed, some experience with the command line & shell, and enough memory to run all of the programs. ... -
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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 them as input of the MaChIAto and refer to the output data of MaChIAto. -
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VisuaR
R-based workflow for the analysis and visualization of sequence data
VisuaR's main goal is to provide a set of analyses and visualizations that are often used in the analyses of amplicon sequencing data. The VisuaR workflow is based on commands from other R packages (e.g. vegan, stringr, plyr, ggplot2), as well as on custom-build scripts. It takes dada2 (https://github.com/benjjneb/dada2) files as input and generates (near-)publication ready figures as output. In addition to NMDS ordinations, cluster dendrograms and UpSet diagrams the workflow features custom scripts that calculate the percentage of singletons or shared ASVs, and visualize diversity indices, or the relative sequence abundance of clades at specific taxonomic levels. ... -
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CRISPRamplicon
A tool for analysis of Genome editing outcomes from sequencing data
...It is faster, cheaper and more accurate than previous techniques of editing DNA and has a wide range of potential applications. Here, a cost-effective and high-throughput strategy was developed for identifying CRISPR/Cas-induced mutations via CRISPR Amplicon Sequencing (Xie’s lab, http://www.biootools.com/). In particular, we have developed a new bioinformatics tool named CRISPRamplicon, which can be used for analysis of CRISPR/Cas9 genome editing outcomes for high-throughput sequencing data with fast speed. -
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MT-Toolbox
Software for molecule tagged DNA sequences
MT-Toolbox is a user friendly software package for analysis of molecule tagged Illumina MiSeq reads. Molecule tagging is a molecular biology technique to significantly reduce amplicon sequence error and PCR bias which can be applied to any amplicon sequencing project. MT-Toolbox converts raw reads into high quality consensus sequences based on each reads molecule tag. For details and other important information please refer to the MT-Toolbox webpage below. MT-Toolbox is now hosted on github here: https://github.com/islandhopper81/mt-toolbox -
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Grinder is a versatile open-source bioinformatic tool to create simulated omic shotgun and amplicon sequence libraries for all main sequencing platforms.
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MT-MT-Toolbox
Metagenomics version of MTToolbox
...These features are not included in the basic version because they only apply to microbial 16S profiling experiments. The standard version of MT-Toolbox can be applied to any amplicon sequencing project where molecule tags are incorporated. For more information on MT-MT-Toolbox and basic features included in MT-Toolbox please refer to the MT-Toolbox webpage (link below). The basic version can be accessed via SourceForge under the name MTToolbox. -
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riboFR-seq
A novel approach to linking 16S rRNA amplicon profiles to metagenomes
...We demonstrated that RiboFR-Seq could detect the vast majority of bacteria not only in well-studied microbiomes but also in novel communities with limited reference genomes. Combined with classical amplicon sequencing and shotgun metagenome sequencing, RiboFR-Seq can link the annotations of 16S rRNA and metagenomic contigs to make a consensus classification. -
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IM-TORNADO
Illinois Mayo Taxonomy Operations for RNA Database Operations
IM-TORNADO HAS MOVED TO GITHUB: https://github.com/pjeraldo/imtornado2 Pipeline for analysis of paired-end 16S rDNA amplicon data. -
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Aspergillus databases for FHiTINGS
This project contains Aspergillus databases for FHiTINGS
This project contains fasta files of ITS, BenA, and CaM sequences for Aspergillus species, which can be used with FHiTINGS program (https://sourceforge.net/projects/fhitings/). Citation Lee, S., Yamamoto, N.* (2015). Accuracy of the high-throughput amplicon sequencing to identify species within the genus Aspergillus, Fungal Biology, in press. -
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Aspergillus databases for FHiTINGS
This project contains alternative databases for FHiTINGS
This project contains fasta files of ITS, BenA, and CaM sequences for Aspergillus species, which can be used with FHiTINGS program (https://sourceforge.net/projects/fhitings/). Citation Lee, S., Yamamoto, N. (2015). Accuracy of the high-throughput amplicon sequencing to identify species within the genus Aspergillus, Fungal Biology, in press. -
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AmpEx
AmpEx Amplicon Extractor
AmpEx is a tool that aims to extract in silico amplicons from high-throughput data. In particular, AmpEx is able to detect amplicons flanked by primer pairs with homopolymer expansions from 454 pyro-reads. -
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simulate_pcr
PCR target prediction software
...This script predicts potential polymerase chain reaction (PCR) amplicons in a large sequence database such as NCBI nt from either singleplex or a large multiplexed set of primers, allowing degenerate primer and probe bases, with target mismatch tolerance and amplicon length range to be set by the user. The PCR amplicon simulation code also annotates amplicons with gene information automatically downloaded from NCBI, and optionally it can predict whether there are also TaqMan/Luminex probe matches within predicted amplicons. It is an open source command line Perl script called simulate_PCR.pl that calls the BLAST (Altschul, et al., 1990) programs makeblastdb, blastn, and blastdbcmd, and the NCBI efetch utility (http://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi). -
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Mutascope
Analysis software designed for PCR-amplicon sequencing data.
Mutascope is a software suite designed to analyze data from high throughput sequencing of PCR amplicons, with an emphasis on normal-tumor comparison for the accurate and sensitive identification of low prevalence mutations. -
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RDP FrameBot is a frameshift correction and nearest neighbor classification tool for use with high-throughput amplicon sequencing. It uses a dynamic programming algorithm to align each query DNA sequence against a set of target protein sequences, produces frameshift-corrected protein and DNA sequences and an optimal global or local protein alignment. It also helps filter out non-target reads. The online version of FrameBot is available on http://fungene.cme.msu.edu/FunGenePipeline, tutorial http://rdp.cme.msu.edu/tutorials/framebot/RDPtutorial_FRAMEBOT.html. ...
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Error-corrector for pyrosequenced amplicon reads.
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.... ++++++++++++++++++++++++++++ De-MetaST = metagenome search tool -output: FASTA file of retrieved amplicons -tutorial video: install_De-MetaST.mp4 De-MetaST-BLAST = metagenome search tool + BLAST -output: (1)FASTA file of retrieved amplicons and (2)TXT file of predicted functions for each amplicon -tutorial videos: (1)install_local_BLAST.mp4 and (2)install_De-MetaST-BLAST.mp4 ++++++++++++++++++++++++++++ All files must first be uncompressed before use. Be sure to read the README.txt files! If you are having trouble downloading a particular file, another source for these files is located on the Google Code project page.
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K-link
Read clustering algorithm which identifies and removes chimeric reads
This project was developed for ESTs. However, there is no reason it cannot be extended for use on amplicon sequences from 454. It is used in conjunction with WCDest clustering software. -
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cangsdb
a stand-alone web-based database tool for processing, managing and ana
CANGS DB is a user-friendly and stand-alone database tool for processing, analyzing and managing the high throughput sequencing data from 454 amplicon resequencing projects. CANGSDB is very easy to use; it could be installed and used on any UNIX based computer to handle individual as well as multiple sequencing projects. It provides full-fledged flexibility with various options in raw sequence processing and analysis. CANGS DB provides a very powerful data retrieval interface, which enables researchers to retrieve sample information and primers and barcodes information from any individual data set or from a combination of data set. ... -
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Amplicon is a Python script for designing PCR primer sets. Amplicon is written in Python 2.3 and Tkinter 8.4. The current script was created for Windows and an executable is available. Future versions of the script should be able to run on Linux and Mac
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TABSAT
Analysis Tool for Targeted Amplicon Bisulfite Sequencing
TABSAT - Targeted Amplicon Bisulfite Sequencing Analysis Tool A tool for analyzing targeted bisulfite sequencing data generated on an Ion Torrent PGM / Illumina MiSeq. The workflow starts with raw sequencing data, performs quality assessment, and uses a tailored version of Bismark to map the reads to a reference genome. Results are aggregated across all samples, presented in table format, and visualized as lollipop plots.
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